1
|
Li Y, Wang J, Li L, Song W, Li M, Hua X, Wang Y, Yuan J, Xue Z. Natural products of pentacyclic triterpenoids: from discovery to heterologous biosynthesis. Nat Prod Rep 2023; 40:1303-1353. [PMID: 36454108 DOI: 10.1039/d2np00063f] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Covering: up to 2022Pentacyclic triterpenoids are important natural bioactive substances that are widely present in plants and fungi. They have significant medicinal efficacy, play an important role in reducing blood glucose and protecting the liver, and have anti-inflammatory, anti-oxidation, anti-fatigue, anti-viral, and anti-cancer activities. Pentacyclic triterpenoids are derived from the isoprenoid biosynthetic pathway, which generates common precursors of triterpenes and steroids, followed by cyclization with oxidosqualene cyclases (OSCs) and decoration via cytochrome P450 monooxygenases (CYP450s) and glycosyltransferases (GTs). Many biosynthetic pathways of triterpenoid saponins have been elucidated by studying their metabolic regulation network through the use of multiomics and identifying their functional genes. Unfortunately, natural resources of pentacyclic triterpenoids are limited due to their low content in plant tissues and the long growth cycle of plants. Based on the understanding of their biosynthetic pathway and transcriptional regulation, plant bioreactors and microbial cell factories are emerging as alternative means for the synthesis of desired triterpenoid saponins. The rapid development of synthetic biology, metabolic engineering, and fermentation technology has broadened channels for the accumulation of pentacyclic triterpenoid saponins. In this review, we summarize the classification, distribution, structural characteristics, and bioactivity of pentacyclic triterpenoids. We further discuss the biosynthetic pathways of pentacyclic triterpenoids and involved transcriptional regulation. Moreover, the recent progress and characteristics of heterologous biosynthesis in plants and microbial cell factories are discussed comparatively. Finally, we propose potential strategies to improve the accumulation of triterpenoid saponins, thereby providing a guide for their future biomanufacturing.
Collapse
Affiliation(s)
- Yanlin Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, PR China
| | - Linyong Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Wenhui Song
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Min Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Xin Hua
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Yu Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, 361102, Fujian, PR China.
| | - Zheyong Xue
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| |
Collapse
|
2
|
Johnson KC, Sabel JL, Cole J, Pruett CL, Plymale R, Reyna NS. From genetics to biotechnology: Synthetic biology as a flexible course-embedded research experience. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:580-591. [PMID: 36053869 PMCID: PMC9826443 DOI: 10.1002/bmb.21662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
The need for changing how science is taught and the expansion of undergraduate research experiences is essential to foster critical thinking in the Natural Sciences. Most faculty research programs only involve a small number of upper-level undergraduate students each semester. The course-based undergraduate research experience (CURE) model enables more students to take ownership over an independent project and experience authentic research. Further, by creating projects that fit into a curriculum's learning goals and student-oriented outcomes, departments help strengthen critical thinking skills in the classroom. Here, we report on the incorporation of a synthetic biology CURE into a mid-level cellular biology course and two advanced level genetics/molecular biology courses. Synthetic biology involves systematic engineering of novel organisms, such as bacteria and plants, to work as functional devices to solve problems in medicine, agriculture, and manufacturing. The value of synthetic biology and its ultimate utility as a teaching tool relies on reusable, standard genetic parts that can be interchanged using common genetic engineering principles. This Synthetic biology CURE effectively achieves five essential goals: (1) a sense of project ownership; (2) self-efficacy: mastery of a manageable number of techniques; (3) increased tolerance for obstacles through challenging research; (4) increased communication skills; and (5) a sense of belonging in a larger scientific community. Based upon our student assessment data, we demonstrate that this course-based synthetic biology laboratory engages students directly in an authentic research experience and models important elements of collaboration, discovery, iteration, and critical thinking.
Collapse
Affiliation(s)
- Kristen C. Johnson
- Department of Life SciencesUniversity of New HampshireManchesterNew HampshireUSA
| | - Jaime L. Sabel
- Department of Biological SciencesUniversity of MemphisMemphisTennesseeUSA
| | - Judith Cole
- Department of Biological SciencesUniversity of MemphisMemphisTennesseeUSA
| | | | - Ruth Plymale
- Department of BiologyOuachita Baptist UniversityArkadelphiaArkansasUSA
| | - Nathan S. Reyna
- Department of BiologyOuachita Baptist UniversityArkadelphiaArkansasUSA
| |
Collapse
|
3
|
de Lorenzo V. Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210395. [PMID: 35757882 PMCID: PMC9234819 DOI: 10.1098/rstb.2021.0395] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
Collapse
Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
| |
Collapse
|
4
|
Heterologous (Over) Expression of Human SoLute Carrier (SLC) in Yeast: A Well-Recognized Tool for Human Transporter Function/Structure Studies. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081206. [PMID: 36013385 PMCID: PMC9410066 DOI: 10.3390/life12081206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/02/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022]
Abstract
For more than 20 years, yeast has been a widely used system for the expression of human membrane transporters. Among them, more than 400 are members of the largest transporter family, the SLC superfamily. SLCs play critical roles in maintaining cellular homeostasis by transporting nutrients, ions, and waste products. Based on their involvement in drug absorption and in several human diseases, they are considered emerging therapeutic targets. Despite their critical role in human health, a large part of SLCs' is 'orphans' for substrate specificity or function. Moreover, very few data are available concerning their 3D structure. On the basis of the human health benefits of filling these knowledge gaps, an understanding of protein expression in systems that allow functional production of these proteins is essential. Among the 500 known yeast species, S. cerevisiae and P. pastoris represent those most employed for this purpose. This review aims to provide a comprehensive state-of-the-art on the attempts of human SLC expression performed by exploiting yeast. The collected data will hopefully be useful for guiding new attempts in SLCs expression with the aim to reveal new fundamental data that could lead to potential effects on human health.
Collapse
|
5
|
Biopolymer production in microbiology by application of metabolic engineering. Polym Bull (Berl) 2022. [DOI: 10.1007/s00289-021-03820-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
6
|
de Lorenzo V. 15 years of microbial biotechnology: the time has come to think big-and act soon. Microb Biotechnol 2022; 15:240-246. [PMID: 34932877 PMCID: PMC8719810 DOI: 10.1111/1751-7915.13993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022] Open
Abstract
Our epoch is largely characterized by the growing realization and concern about the reality of climate change and environmental deterioration, the surge of global pandemics, the unacceptable inequalities between developed and underdeveloped countries and their unavoidable translation into messy immigration, overpopulation and food crises. While all of these issues have a fundamentally political core, they are not altogether removed from the fact that Earth is primarily a microbial planet and microorganisms are the key agents that make the biosphere (including ourselves) function as it does. It thus makes sense that we bring the microbial world-that is the environmental microbiome-to the necessary multi-tiered conversation (hopefully followed by action) on how to avoid future threats and how to make our globe a habitable common house. Beyond discussion on governance, such a dialogue has technical and scientific aspects that only frontline microbial biotechnology can help to tackle. Fortunately, the field has witnessed the onset of new conceptual and material tools that were missing when the journal started.
Collapse
|
7
|
Wu J, Wang X, Xiao L, Wang F, Zhang Y, Li X. Synthetic Protein Scaffolds for Improving R-(-)-Linalool Production in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5663-5670. [PMID: 33983023 DOI: 10.1021/acs.jafc.1c01101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
R-(-)-Linalool is widely used in the pharmaceutical, agrochemical, and fragrance industries; however, its applications are limited owing to low yield and high cost of production. To improve the production efficiency of R-(-)-linalool in Escherichia coli, three enzymes [E. coli-derived isopentenyl diphosphate isomerase, Abies grandis-derived geranyl diphosphate synthase, and Streptomyces clavuligerus-derived (3R)-linalool synthases] were physically colocalized to synthetic complexes using synthetic protein scaffolds of GTPase-binding domain, Src homology 3, and PSD95/DlgA/Zo-1. R-(-)-Linalool was produced at the highest concentration in the strain IGL114 containing a scaffold ratio of 1:1:4. By further optimizing the inducer, temperature, and glycerol concentration, the production titer of R-(-)-linalool in the shake flask was increased by approximately 10 times compared with that of the scaffold-free control and was 2.78 times the previously reported yield. The production in the fermenter was about 1.5 times the previous highest production. In general, the final strain accumulated 277.8 and 1523.2 mg/L R-(-)-linalool under the conditions of shake-flask and fed-batch fermentation, respectively. This study provides a foundation for the assembly of bacterial intracellular protein scaffolds.
Collapse
Affiliation(s)
- Jing Wu
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Xun Wang
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Longjie Xiao
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Fei Wang
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Yu Zhang
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Xun Li
- Jiangsu Provincial Key Laboratory for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Key Laboratory of Biomass-Based Green Fuels and Chemicals, Nanjing Forestry University, Nanjing 210037, China
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
- International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| |
Collapse
|
8
|
Wu H, Yang J, Shen P, Li Q, Wu W, Jiang X, Qin L, Huang J, Cao X, Qi F. High-Level Production of Indole-3-acetic Acid in the Metabolically Engineered Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1916-1924. [PMID: 33541074 DOI: 10.1021/acs.jafc.0c08141] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Indole-3-acetic acid (IAA) is a critical plant hormone that regulates cell division, development, and metabolism. IAA synthesis in plants and plant-associated microorganisms cannot fulfill the requirement for large-scale agricultural production. Here, two novel IAA biosynthesis pathways, tryptamine (TAM) and indole-3-acetamide (IAM), were developed for IAA production by whole-cell catalysis and de novo biosynthesis in an engineered Escherichia coli MG1655. When 10 g/L l-tryptophan was used as a substrate, an MIA-6 strain containing a heterologous IAM pathway had the highest IAA titer of 7.10 g/L (1.34 × 103 mg/g DCW), which was 98.4 times more than MTAI-5 containing the TAM pathway by whole-cell catalysis. De novo IAA biosynthesis was optimized by improving NAD(P)H availability, resulting in an increased IAA titer of 906 mg/L obtained by the MGΔadhE::icd strain, which is 29.7% higher than the control. These strategies exhibit the potential for IAA production in engineered E. coli and possible industrial applications.
Collapse
Affiliation(s)
- Hongxuan Wu
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Jinhua Yang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Peijie Shen
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Qingchen Li
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation and Provincial University Engineering Research Center of Industrial Biocatalysis, Fujian Normal University, Fuzhou, Fujian 350117, China
| | - Weibin Wu
- Fujian Vocational College of Bio-engineering, Fuzhou, Fujian 350002, China
| | - Xianzhang Jiang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Lina Qin
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| | - Xiao Cao
- Fujian Vocational College of Bio-engineering, Fuzhou, Fujian 350002, China
| | - Feng Qi
- Engineering Research Center of Industrial Microbiology of Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou 350117, Fujian, China
| |
Collapse
|
9
|
Xu Y, Zhou D, Luo R, Yang X, Wang B, Xiong X, Shen W, Wang D, Wang Q. Metabolic engineering of Escherichia coli for polyamides monomer δ-valerolactam production from feedstock lysine. Appl Microbiol Biotechnol 2020; 104:9965-9977. [PMID: 33064187 DOI: 10.1007/s00253-020-10939-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 09/06/2020] [Accepted: 10/01/2020] [Indexed: 01/03/2023]
Abstract
Nylon 5 and nylon 6,5 are recently explored as new commercial polyamides, of which the monomer includes δ-valerolactam. In this study, a novel catalytic activity of lysine 2-monooxygenase (DavB) was explored to produce δ-valerolactam from L-pipecolic acid (L-PA), functioning as oxidative decarboxylase on a cyclic compound. Recombinant Escherichia coli BS01 strain expressing DavB from Pseudomonas putida could synthesize δ-valerolactam from L-pipecolic acid with a concentration of 90.3 mg/L. Through the co-expression of recombinant apoptosis-inducing protein (rAIP) from Scomber japonicus, glucose dehydrogenase (GDH) from Bacillus subtilis, Δ1-piperideine-2-carboxylae reductase (DpkA) from P. putida and lysine permease (LysP) from E. coli with DavB, δ-valerolactam was produced with the highest concentration of 242 mg/L. α-Dioxygenases (αDox) from Oryza sativa could act as a similar catalyst on L-pipecolic acid. A novel δ-valerolactam synthesis pathway was constructed entirely via microbial conversion from feedstock lysine in this study. Our system has great potential in the development of a bio-nylon production process. KEY POINTS: • DavB performs as an oxidative decarboxylase on L-PA with substrate promiscuity. • Strain with rAIP, GDH, DpkA, LysP, and DavB coexpression could produce δ-valerolactam. • This is the first time to obtain valerolactam entirely via biosynthesis from lysine.
Collapse
Affiliation(s)
- Yanqin Xu
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Process for Clean Energy and Resource Utilization, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Dan Zhou
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Process for Clean Energy and Resource Utilization, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Ruoshi Luo
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Process for Clean Energy and Resource Utilization, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Xizhi Yang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Process for Clean Energy and Resource Utilization, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Baosheng Wang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Process for Clean Energy and Resource Utilization, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, 99164-6120, USA
| | - Weifeng Shen
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Process for Clean Energy and Resource Utilization, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Dan Wang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Key Laboratory of Chemical Process for Clean Energy and Resource Utilization, Chongqing University, Chongqing, 401331, People's Republic of China.
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
| |
Collapse
|
10
|
Dasgupta A, Chowdhury N, De RK. Metabolic pathway engineering: Perspectives and applications. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 192:105436. [PMID: 32199314 DOI: 10.1016/j.cmpb.2020.105436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Metabolic engineering aims at contriving microbes as biocatalysts for enhanced and cost-effective production of countless secondary metabolites. These secondary metabolites can be treated as the resources of industrial chemicals, pharmaceuticals and fuels. Plants are also crucial targets for metabolic engineers to produce necessary secondary metabolites. Metabolic engineering of both microorganism and plants also contributes towards drug discovery. In order to implement advanced metabolic engineering techniques efficiently, metabolic engineers should have detailed knowledge about cell physiology and metabolism. Principle behind methodologies: Genome-scale mathematical models of integrated metabolic, signal transduction, gene regulatory and protein-protein interaction networks along with experimental validation can provide such knowledge in this context. Incorporation of omics data into these models is crucial in the case of drug discovery. Inverse metabolic engineering and metabolic control analysis (MCA) can help in developing such models. Artificial intelligence methodology can also be applied for efficient and accurate metabolic engineering. CONCLUSION In this review, we discuss, at the beginning, the perspectives of metabolic engineering and its application on microorganism and plant leading to drug discovery. At the end, we elaborate why inverse metabolic engineering and MCA are closely related to modern metabolic engineering. In addition, some crucial steps ensuring efficient and optimal metabolic engineering strategies have been discussed. Moreover, we explore the use of genomics data for the activation of silent metabolic clusters and how it can be integrated with metabolic engineering. Finally, we exhibit a few applications of artificial intelligence to metabolic engineering.
Collapse
Affiliation(s)
- Abhijit Dasgupta
- Department of Data Science, School of Interdisciplinary Studies, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India
| | - Nirmalya Chowdhury
- Department of Computer Science & Engineering, Jadavpur University, Kolkata 700032, India
| | - Rajat K De
- Machine Intelligence Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700108, India.
| |
Collapse
|
11
|
Li S, Jendresen CB, Landberg J, Pedersen LE, Sonnenschein N, Jensen SI, Nielsen AT. Genome-Wide CRISPRi-Based Identification of Targets for Decoupling Growth from Production. ACS Synth Biol 2020; 9:1030-1040. [PMID: 32268068 DOI: 10.1021/acssynbio.9b00143] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Growth decoupling can be used to optimize microbial production of biobased compounds by inhibiting excess biomass formation and redirect carbon flux from growth to product formation. However, identifying suitable genetic targets through rational design is challenging. Here, we conduct a genome-wide CRISPRi screen to discover growth switches suitable for decoupling growth and production. Using an sgRNA library covering 12 238 loci in the Escherichia coli genome, we screen for targets that inhibit growth while allowing for continued protein production. In total, we identify 1332 sgRNAs that simultaneously decrease growth and maintain or increase accumulation of GFP. The top target sibB/ibsB shows more than 5-fold increase in GFP accumulation and 45% decrease in biomass formation. Overall, our genome-wide CRISPRi screen provides key targets for growth decoupling, and the approach can be applied to improve biobased production in other microorganisms.
Collapse
Affiliation(s)
- Songyuan Li
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Christian Bille Jendresen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- CysBio ApS, Agern Allé 1, 2970 Hørsholm, Denmark
| | - Jenny Landberg
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Nikolaus Sonnenschein
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Sheila Ingemann Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, 2800 Kongens Lyngby, Denmark
- CysBio ApS, Agern Allé 1, 2970 Hørsholm, Denmark
| |
Collapse
|
12
|
Luo Z, Hoffmann SA, Jiang S, Cai Y, Dai J. Probing eukaryotic genome functions with synthetic chromosomes. Exp Cell Res 2020; 390:111936. [PMID: 32165165 DOI: 10.1016/j.yexcr.2020.111936] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/25/2020] [Accepted: 02/29/2020] [Indexed: 02/07/2023]
Abstract
The ability to redesign and reconstruct a cell at whole-genome level provides new platforms for biological study. The international synthetic yeast genome project-Sc2.0, designed by interrogating knowledge amassed by the yeast community to date, exemplifies how a classical synthetic biology "design-build-test-learn" engineering cycle can effectively test hypotheses about various genome fundamentals. The genome reshuffling SCRaMbLE system implemented in synthetic yeast strains also provides unprecedented diversified resources for genotype-phenotype study and yeast metabolic engineering. Further development of genome synthesis technology will shed new lights on complex biological processes in higher eukaryotes.
Collapse
Affiliation(s)
- Zhouqing Luo
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Stefan A Hoffmann
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK
| | - Shuangying Jiang
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yizhi Cai
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, Manchester, UK.
| | - Junbiao Dai
- Guangdong Provincial Key Laboratory of Synthetic Genomics, Shenzhen Key Laboratory of Synthetic Genomics, Center for Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China; College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518055, China.
| |
Collapse
|
13
|
Metabolic engineering for the production of dicarboxylic acids and diamines. Metab Eng 2020; 58:2-16. [DOI: 10.1016/j.ymben.2019.03.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 11/18/2022]
|
14
|
Kasbawati, Kalondeng A, Sulfahri. A numerical study of the sensitivity of ethanol flux to the existence of co-factors in the Central metabolism of a yeast cell using multi-substrate enzymes kinetic modelling. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1758593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Kasbawati
- Department of Mathematics, Universitas Hasanuddin, Makassar, Indonesia
| | - Anisa Kalondeng
- Department of Statistics, Universitas Hasanuddin, Makassar, Indonesia
| | - Sulfahri
- Department of Biology, Universitas Hasanuddin, Makassar, Indonesia
| |
Collapse
|
15
|
Rennig M, Mundhada H, Wordofa GG, Gerngross D, Wulff T, Worberg A, Nielsen AT, Nørholm MHH. Industrializing a Bacterial Strain for l-Serine Production through Translation Initiation Optimization. ACS Synth Biol 2019; 8:2347-2358. [PMID: 31550142 DOI: 10.1021/acssynbio.9b00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Turning a proof-of-concept synthetic biology design into a robust, high performing cell factory is a major time and money consuming task, which severely limits the growth of the white biotechnology sector. Here, we extend the use of tunable antibiotic resistance markers for synthetic evolution (TARSyn), a workflow for screening translation initiation region (TIR) libraries with antibiotic selection, to generic pathway engineering, and transform a proof-of-concept synbio design into a process that performs at industrially relevant levels. Using a combination of rational design and adaptive evolution, we recently engineered a high-performing bacterial strain for production of the important building block biochemical l-serine, based on two high-copy pET vectors facilitating expression of the serine biosynthetic genes serA, serC, and serB from three independent transcriptional units. Here, we prepare the bacterial strain for industrial scale up by transferring and reconfiguring the three genes into an operon encoded on a single low-copy plasmid. Not surprisingly, this initially reduces production titers considerably. We use TARSyn to screen both experimental and computational optimization designs resulting in high-performing synthetic serine operons and reach industrially relevant production levels of 50 g/L in fed-batch fermentations, the highest reported so far for serine production.
Collapse
Affiliation(s)
- Maja Rennig
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
| | - Hemanshu Mundhada
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Gossa G. Wordofa
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Daniel Gerngross
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Andreas Worberg
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
| | - Alex T. Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
| | - Morten H. H. Nørholm
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs. Lyngby, Denmark
- Mycropt IVS, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
16
|
Shrestha B, Pandey RP, Darsandhari S, Parajuli P, Sohng JK. Combinatorial approach for improved cyanidin 3-O-glucoside production in Escherichia coli. Microb Cell Fact 2019; 18:7. [PMID: 30654816 PMCID: PMC6335687 DOI: 10.1186/s12934-019-1056-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 01/07/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Multi-monocistronic and multi-variate vectors were designed, built, and tested for the improved production of cyanidin 3-O-glucoside (C3G) in Escherichia coli BL21 (DE3). The synthetic bio-parts were designed in such a way that multiple genes can be assembled using the bio-brick system, and expressed under different promoters in a single vector. The vectors harbor compatible cloning sites, so that the genes can be shuffled from one vector to another in a single step, and assembled into a single vector. The two required genes: anthocyanidin synthase (PhANS) from Petunia hybrida, and cyanidin 3-O-glucosyltransferase (At3GT) from Arabidopsis thaliana, were individually cloned under PT7, Ptrc, and PlacUV5 promoters. Both PhANS and At3GT were shuffled back and forth, so as to generate a combinatorial system for C3G production. The constructed systems were further coupled with the genes for UDP-D-glucose synthesis, all cloned in a multi-monocistronic fashion under PT7. Finally, the production of C3G was checked and confirmed using the modified M9 media, and analyzed through various chromatography and spectrometric analyses. RESULTS The engineered strains endowed with newly generated vectors and the genes for C3G biosynthesis and UDP-D-glucose synthesis were fed with 2 mM (+)-catechin and D-glucose for the production of cyanidin, and its subsequent conversion to C3G. One of the engineered strains harboring At3GT and PhANS under Ptrc promoter and UDP-D-glucose biosynthesis genes under PT7 promoter led to the production of ~ 439 mg/L of C3G within 36 h of incubation, when the system was exogenously fed with 5% (w/v) D-glucose. This system did not require exogenous supplementation of UDP-D-glucose. CONCLUSION A synthetic vector system using different promoters has been developed and used for the synthesis of C3G in E. coli BL21 (DE3) by directing the metabolic flux towards the UDP-D-glucose. This system has the potential of generating better strains for the synthesis of valuable natural products.
Collapse
Affiliation(s)
- Biplav Shrestha
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460 Republic of Korea
| | - Ramesh Prasad Pandey
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460 Republic of Korea
- Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460 Republic of Korea
| | - Sumangala Darsandhari
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460 Republic of Korea
| | - Prakash Parajuli
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460 Republic of Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460 Republic of Korea
- Department of BT-Convergent Pharmaceutical Engineering, SunMoon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam 31460 Republic of Korea
| |
Collapse
|
17
|
Kasbawati, Agnes, Kalondeng A, Sulfahri. Mathematical study of feedback inhibition effects on the dynamics of metabolites on the central metabolism of a yeast cell: a combination of kinetic model and metabolic control analysis. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1641148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Kasbawati
- Applied Mathematics Laboratory, Department of Mathematics, Hasanuddin University, Makassar, Indonesia
| | - Agnes
- Applied Mathematics Laboratory, Department of Mathematics, Hasanuddin University, Makassar, Indonesia
| | - Anisa Kalondeng
- Applied Mathematics Laboratory, Department of Mathematics, Hasanuddin University, Makassar, Indonesia
| | - Sulfahri
- Microbiology Laboratory, Department of Biology, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, Indonesia
| |
Collapse
|
18
|
Abstract
Synthetic biology has undergone dramatic advancements for over a decade, during which it has expanded our understanding on the systems of life and opened new avenues for microbial engineering. Many biotechnological and computational methods have been developed for the construction of synthetic systems. Achievements in synthetic biology have been widely adopted in metabolic engineering, a field aimed at engineering micro-organisms to produce substances of interest. However, the engineering of metabolic systems requires dynamic redistribution of cellular resources, the creation of novel metabolic pathways, and optimal regulation of the pathways to achieve higher production titers. Thus, the design principles and tools developed in synthetic biology have been employed to create novel and flexible metabolic pathways and to optimize metabolic fluxes to increase the cells’ capability to act as production factories. In this review, we introduce synthetic biology tools and their applications to microbial cell factory constructions.
Collapse
|
19
|
Metabolic engineering of Escherichia coli for de novo biosynthesis of vitamin B 12. Nat Commun 2018; 9:4917. [PMID: 30464241 PMCID: PMC6249242 DOI: 10.1038/s41467-018-07412-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/01/2018] [Indexed: 11/30/2022] Open
Abstract
The only known source of vitamin B12 (adenosylcobalamin) is from bacteria and archaea. Here, using genetic and metabolic engineering, we generate an Escherichia coli strain that produces vitamin B12 via an engineered de novo aerobic biosynthetic pathway. In vitro and/or in vivo analysis of genes involved in adenosylcobinamide phosphate biosynthesis from Rhodobacter capsulatus suggest that the biosynthetic steps from co(II)byrinic acid a,c-diamide to adocobalamin are the same in both the aerobic and anaerobic pathways. Finally, we increase the vitamin B12 yield of a recombinant E. coli strain by more than ∼250-fold to 307.00 µg g−1 DCW via metabolic engineering and optimization of fermentation conditions. Beyond our demonstration of E. coli as a microbial biosynthetic platform for vitamin B12 production, our study offers an encouraging example of how the several dozen proteins of a complex biosynthetic pathway can be transferred between organisms to facilitate industrial production. Vitamin B12 is an essential nutrient with limited natural sources. Here the authors transfer 28 pathway synthesis genes from several bacteria including R. capsulatus to E. coli and, using metabolic engineering and optimised fermentation conditions, achieve high yields.
Collapse
|
20
|
Yu JL, Qian ZG, Zhong JJ. Advances in bio-based production of dicarboxylic acids longer than C4. Eng Life Sci 2018; 18:668-681. [PMID: 32624947 DOI: 10.1002/elsc.201800023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/18/2018] [Accepted: 06/13/2018] [Indexed: 12/15/2022] Open
Abstract
Growing concerns of environmental pollution and fossil resource shortage are major driving forces for bio-based production of chemicals traditionally from petrochemical industry. Dicarboxylic acids (DCAs) are important platform chemicals with large market and wide applications, and here the recent advances in bio-based production of straight-chain DCAs longer than C4 from biological approaches, especially by synthetic biology, are reviewed. A couple of pathways were recently designed and demonstrated for producing DCAs, even those ranging from C5 to C15, by employing respective starting units, extending units, and appropriate enzymes. Furthermore, in order to achieve higher production of DCAs, enormous efforts were made in engineering microbial hosts that harbored the biosynthetic pathways and in improving properties of biocatalytic elements to enhance metabolic fluxes toward target DCAs. Here we summarize and discuss the current advantages and limitations of related pathways, and also provide perspectives on synthetic pathway design and optimization for hyper-production of DCAs.
Collapse
Affiliation(s)
- Jia-Le Yu
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai P. R. China.,State Key Laboratory of Bioreactor Engineering, School of Biotechnology East China University of Science and Technology Shanghai P. R. China
| | - Zhi-Gang Qian
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai P. R. China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) East China University of Science and Technology Shanghai P. R. China
| | - Jian-Jiang Zhong
- State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai P. R. China.,State Key Laboratory of Bioreactor Engineering, School of Biotechnology East China University of Science and Technology Shanghai P. R. China.,Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT) East China University of Science and Technology Shanghai P. R. China
| |
Collapse
|
21
|
Blount BA, Gowers GOF, Ho JCH, Ledesma-Amaro R, Jovicevic D, McKiernan RM, Xie ZX, Li BZ, Yuan YJ, Ellis T. Rapid host strain improvement by in vivo rearrangement of a synthetic yeast chromosome. Nat Commun 2018; 9:1932. [PMID: 29789540 PMCID: PMC5964169 DOI: 10.1038/s41467-018-03143-w] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/23/2018] [Indexed: 11/21/2022] Open
Abstract
Synthetic biology tools, such as modular parts and combinatorial DNA assembly, are routinely used to optimise the productivity of heterologous metabolic pathways for biosynthesis or substrate utilisation, yet it is well established that host strain background is just as important for determining productivity. Here we report that in vivo combinatorial genomic rearrangement of Saccharomyces cerevisiae yeast with a synthetic chromosome V can rapidly generate new, improved host strains with genetic backgrounds favourable to diverse heterologous pathways, including those for violacein and penicillin biosynthesis and for xylose utilisation. We show how the modular rearrangement of synthetic chromosomes by SCRaMbLE can be easily determined using long-read nanopore sequencing and we explore experimental conditions that optimise diversification and screening. This synthetic genome approach to metabolic engineering provides productivity improvements in a fast, simple and accessible way, making it a valuable addition to existing strain improvement techniques. The Sc2.0 project has built the Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) system into their synthetic chromosomes. Here the authors use SCRaMbLE to rapidly develop, diversify and screen strains for diverse production and growth characteristics.
Collapse
Affiliation(s)
- B A Blount
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - G-O F Gowers
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - J C H Ho
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - R Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - D Jovicevic
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - R M McKiernan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Z X Xie
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, PR China
| | - B Z Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, PR China
| | - Y J Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, 300072, Tianjin, PR China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, 300072, Tianjin, PR China
| | - T Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK. .,Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| |
Collapse
|
22
|
Liang X, Li C, Wang W, Li Q. Integrating T7 RNA Polymerase and Its Cognate Transcriptional Units for a Host-Independent and Stable Expression System in Single Plasmid. ACS Synth Biol 2018; 7:1424-1435. [PMID: 29609457 DOI: 10.1021/acssynbio.8b00055] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metabolic engineering and synthetic biology usually require universal expression systems for stable and efficient gene expression in various organisms. In this study, a host-independent and stable T7 expression system had been developed by integrating T7 RNA polymerase and its cognate transcriptional units in single plasmid. The expression of T7 RNA polymerase was restricted below its lethal threshold using a T7 RNA polymerase antisense gene cassette, which allowed long periods of cultivation and protein production. In addition, by designing ribosome binding sites, we further tuned the expression capacity of this novel T7 system within a wide range. This host-independent expression system efficiently expressed genes in five different Gram-negative strains and one Gram-positive strain and was also shown to be applicable in a real industrial d- p-hydroxyphenylglycine production system.
Collapse
Affiliation(s)
- Xiao Liang
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Chenmeng Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wenya Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Qiang Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| |
Collapse
|
23
|
Karim AS, Heggestad JT, Crowe SA, Jewett MC. Controlling cell-free metabolism through physiochemical perturbations. Metab Eng 2017; 45:86-94. [PMID: 29155060 DOI: 10.1016/j.ymben.2017.11.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/03/2017] [Accepted: 11/11/2017] [Indexed: 10/18/2022]
Abstract
Building biosynthetic pathways and engineering metabolic reactions in cells can be time-consuming due to complexities in cellular metabolism. These complexities often convolute the combinatorial testing of biosynthetic pathway designs needed to define an optimal biosynthetic system. To simplify the optimization of biosynthetic systems, we recently reported a new cell-free framework for pathway construction and testing. In this framework, multiple crude-cell extracts are selectively enriched with individual pathway enzymes, which are then mixed to construct full biosynthetic pathways on the time scale of a day. This rapid approach to building pathways aids in the study of metabolic pathway performance by providing a unique freedom of design to modify and control biological systems for both fundamental and applied biotechnology. The goal of this work was to demonstrate the ability to probe biosynthetic pathway performance in our cell-free framework by perturbing physiochemical conditions, using n-butanol synthesis as a model. We carried out three unique case studies. First, we demonstrated the power of our cell-free approach to maximize biosynthesis yields by mapping physiochemical landscapes using a robotic liquid-handler. This allowed us to determine that NAD and CoA are the most important factors that govern cell-free n-butanol metabolism. Second, we compared metabolic profile differences between two different approaches for building pathways from enriched lysates, heterologous expression and cell-free protein synthesis. We discover that phosphate from PEP utilization, along with other physiochemical reagents, during cell-free protein synthesis-coupled, crude-lysate metabolic system operation inhibits optimal cell-free n-butanol metabolism. Third, we show that non-phosphorylated secondary energy substrates can be used to fuel cell-free protein synthesis and n-butanol biosynthesis. Taken together, our work highlights the ease of using cell-free systems to explore physiochemical perturbations and suggests the need for a more controllable, multi-step, separated cell-free framework for future pathway prototyping and enzyme discovery efforts.
Collapse
Affiliation(s)
- Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Jacob T Heggestad
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Samantha A Crowe
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA; Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL 60611, USA; Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA.
| |
Collapse
|
24
|
Yu JL, Xia XX, Zhong JJ, Qian ZG. Enhanced production of C5 dicarboxylic acids by aerobic-anaerobic shift in fermentation of engineered Escherichia coli. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
25
|
Das A, Verma A, Mukherjee KJ. Synthesis of dopamine in E. coli using plasmid-based expression system and its marked effect on host growth profiles. Prep Biochem Biotechnol 2017; 47:754-760. [PMID: 28430025 DOI: 10.1080/10826068.2017.1320291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
L-Dopa and dopamine are important pathway intermediates toward the synthesis of catecholamine such as epinephrine and norepinephrine from amino acid L-tyrosine. Dopamine, secreted from dopaminergic nerve cells, serves as an important neurotransmitter. We report the synthesis of dopamine by extending the aromatic amino acid pathway of Escherichia coli DH5α by the expression of 4-hydroxyphenylacetate-3-hydrolase (HpaBC) from E. coli and an engineered dopa decarboxylase (DDC) from pig kidney cell. The activity of HpaBC and DDC require 200 µM iron supplementation and 50 µM vitamin B6, respectively as additives to the growth media. The maximum concentration of L-dopa and dopamine obtained from the broth was around 26 and 27 mg/L after 24 hr of separate shake flask studies. We observed that in the presence of dopamine synthesized in vivo host growth was remarkably enhanced. These observations lead us to an interesting finding about the role of these catecholamines on bacterial growth. It is clear that synthesis of dopamine in vivo actually promotes growth much efficiently as compared to when dopamine is added to the system from outside. From HPLC and GC-MS data it was further observed that L-dopa was stable within the observable time of experiments whereas dopamine actually was subjected to degradation via oxidation and host consumption.
Collapse
Affiliation(s)
- Arunangshu Das
- a School of Biotechnology , Jawaharlal Nehru University , New Delhi , India
| | - Anita Verma
- a School of Biotechnology , Jawaharlal Nehru University , New Delhi , India
| | | |
Collapse
|
26
|
Iman M, Sobati T, Panahi Y, Mobasheri M. Systems Biology Approach to Bioremediation of Nitroaromatics: Constraint-Based Analysis of 2,4,6-Trinitrotoluene Biotransformation by Escherichia coli. Molecules 2017; 22:E1242. [PMID: 28805729 PMCID: PMC6152126 DOI: 10.3390/molecules22081242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 06/22/2017] [Accepted: 06/23/2017] [Indexed: 01/02/2023] Open
Abstract
Microbial remediation of nitroaromatic compounds (NACs) is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli) has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT). Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E. coli to account for a curated version of major TNT transformation pathways known or evidently hypothesized to be active in E. coli in present of TNT. Using constraint-based analysis (CBA) methods, we then performed several series of in silico experiments to elucidate the contribution of these pathways individually or in combination to the E. coli TNT transformation capacity. Results of our analyses were validated by replicating several experimentally observed TNT degradation phenotypes in E. coli cultures. We further used the extended model to explore the influence of process parameters, including aeration regime, TNT concentration, cell density, and carbon source on TNT degradation efficiency. We also conducted an in silico metabolic engineering study to design a series of E. coli mutants capable of degrading TNT at higher yield compared with the wild-type strain. Our study, therefore, extends the application of CBA to bioremediation of nitroaromatics and demonstrates the usefulness of this approach to inform bioremediation research.
Collapse
Affiliation(s)
- Maryam Iman
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
- Department of Pharmaceutics, School of Pharmacy, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
| | - Tabassom Sobati
- Young Researchers and Elite Club, Islamic Azad University, 46115655 Tehran, Iran.
| | - Yunes Panahi
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, 1477893855 Tehran, Iran.
| | - Meysam Mobasheri
- Young Researchers and Elite Club, Islamic Azad University, 46115655 Tehran, Iran.
- Department of Biotechnology, Faculty of Advanced Sciences & Technology, Pharmaceutical Sciences Branch, Islamic Azad University (IAUPS), 194193311 Tehran, Iran.
| |
Collapse
|
27
|
Guzmán-Trampe S, Ceapa CD, Manzo-Ruiz M, Sánchez S. Synthetic biology era: Improving antibiotic’s world. Biochem Pharmacol 2017; 134:99-113. [DOI: 10.1016/j.bcp.2017.01.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/26/2017] [Indexed: 12/12/2022]
|
28
|
Englaender JA, Jones JA, Cress BF, Kuhlman TE, Linhardt RJ, Koffas MAG. Effect of Genomic Integration Location on Heterologous Protein Expression and Metabolic Engineering in E. coli. ACS Synth Biol 2017; 6:710-720. [PMID: 28055177 DOI: 10.1021/acssynbio.6b00350] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Chromosomal integration offers a selection-free alternative to DNA plasmids for expression of foreign proteins and metabolic pathways. Episomal plasmid DNA is convenient but has drawbacks including increased metabolic burden and the requirement for selection in the form of antibiotics. E. coli has long been used for the expression of foreign proteins and for the production of valuable metabolites by expression of complete metabolic pathways. The gene encoding the fluorescent reporter protein mCherry was integrated into four genomic loci on the E. coli chromosome to measure protein expression at each site. Expression levels ranged from 25% to 500% compared to the gene expressed on a high-copy plasmid. Modular expression of DNA is one of the most commonly used methods for optimizing metabolite production by metabolic engineering. By combining a recently developed method for integration of large synthetic DNA constructs into the genome, we were able to integrate two foreign pathways into the same four genomic loci. We have demonstrated that only one of the genomic loci resulted in the production of violacein, and that all four loci produced trans-cinnamic acid from the TAL pathway.
Collapse
Affiliation(s)
- Jacob A Englaender
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - J Andrew Jones
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Chemistry, Hamilton College , Clinton, New York 13323, United States
| | - Brady F Cress
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Thomas E Kuhlman
- Department of Physics, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Carl. R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Robert J Linhardt
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Mattheos A G Koffas
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| |
Collapse
|
29
|
Ghosh IN, Landick R. OptSSeq: High-Throughput Sequencing Readout of Growth Enrichment Defines Optimal Gene Expression Elements for Homoethanologenesis. ACS Synth Biol 2016; 5:1519-1534. [PMID: 27404024 DOI: 10.1021/acssynbio.6b00121] [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] [Indexed: 11/28/2022]
Abstract
The optimization of synthetic pathways is a central challenge in metabolic engineering. OptSSeq (Optimization by Selection and Sequencing) is one approach to this challenge. OptSSeq couples selection of optimal enzyme expression levels linked to cell growth rate with high-throughput sequencing to track enrichment of gene expression elements (promoters and ribosome-binding sites) from a combinatorial library. OptSSeq yields information on both optimal and suboptimal enzyme levels, and helps identify constraints that limit maximal product formation. Here we report a proof-of-concept implementation of OptSSeq using homoethanologenesis, a two-step pathway consisting of pyruvate decarboxylase (Pdc) and alcohol dehydrogenase (Adh) that converts pyruvate to ethanol and is naturally optimized in the bacterium Zymomonas mobilis. We used OptSSeq to determine optimal gene expression elements and enzyme levels for Z. mobilis Pdc, AdhA, and AdhB expressed in Escherichia coli. By varying both expression signals and gene order, we identified an optimal solution using only Pdc and AdhB. We resolved current uncertainty about the functions of the Fe2+-dependent AdhB and Zn2+-dependent AdhA by showing that AdhB is preferred over AdhA for rapid growth in both E. coli and Z. mobilis. Finally, by comparing predictions of growth-linked metabolic flux to enzyme synthesis costs, we established that optimal E. coli homoethanologenesis was achieved by our best pdc-adhB expression cassette and that the remaining constraints lie in the E. coli metabolic network or inefficient Pdc or AdhB function in E. coli. OptSSeq is a general tool for synthetic biology to tune enzyme levels in any pathway whose optimal function can be linked to cell growth or survival.
Collapse
Affiliation(s)
- Indro Neil Ghosh
- DOE
Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin 53726, United States
| | - Robert Landick
- DOE
Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin 53726, United States
| |
Collapse
|
30
|
Kim SK, Han GH, Seong W, Kim H, Kim SW, Lee DH, Lee SG. CRISPR interference-guided balancing of a biosynthetic mevalonate pathway increases terpenoid production. Metab Eng 2016; 38:228-240. [DOI: 10.1016/j.ymben.2016.08.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/10/2016] [Accepted: 08/24/2016] [Indexed: 11/26/2022]
|
31
|
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]
|
32
|
Yang S, Fei Q, Zhang Y, Contreras LM, Utturkar SM, Brown SD, Himmel ME, Zhang M. Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microb Biotechnol 2016; 9:699-717. [PMID: 27629544 PMCID: PMC5072187 DOI: 10.1111/1751-7915.12408] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 12/04/2022] Open
Abstract
Zymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.
Collapse
Affiliation(s)
- Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Qiang Fei
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yaoping Zhang
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - Sagar M Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA
| | - Steven D Brown
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
| |
Collapse
|
33
|
Carbonell P, Currin A, Jervis AJ, Rattray NJW, Swainston N, Yan C, Takano E, Breitling R. Bioinformatics for the synthetic biology of natural products: integrating across the Design-Build-Test cycle. Nat Prod Rep 2016; 33:925-32. [PMID: 27185383 PMCID: PMC5063057 DOI: 10.1039/c6np00018e] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 12/11/2022]
Abstract
Covering: 2000 to 2016Progress in synthetic biology is enabled by powerful bioinformatics tools allowing the integration of the design, build and test stages of the biological engineering cycle. In this review we illustrate how this integration can be achieved, with a particular focus on natural products discovery and production. Bioinformatics tools for the DESIGN and BUILD stages include tools for the selection, synthesis, assembly and optimization of parts (enzymes and regulatory elements), devices (pathways) and systems (chassis). TEST tools include those for screening, identification and quantification of metabolites for rapid prototyping. The main advantages and limitations of these tools as well as their interoperability capabilities are highlighted.
Collapse
Affiliation(s)
- Pablo Carbonell
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Andrew Currin
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Adrian J. Jervis
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Nicholas J. W. Rattray
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Neil Swainston
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Cunyu Yan
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Eriko Takano
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| | - Rainer Breitling
- Manchester Centre for Fine and Specialty Chemicals (SYNBIOCHEM) , Manchester Institute of Biotechnology , University of Manchester , Manchester M1 7DN , UK . ;
| |
Collapse
|
34
|
Dhakal D, Chaudhary AK, Yi JS, Pokhrel AR, Shrestha B, Parajuli P, Shrestha A, Yamaguchi T, Jung HJ, Kim SY, Kim BG, Sohng JK. Enhanced production of nargenicin A1 and creation of a novel derivative using a synthetic biology platform. Appl Microbiol Biotechnol 2016; 100:9917-9931. [PMID: 27412463 DOI: 10.1007/s00253-016-7705-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/19/2016] [Accepted: 06/23/2016] [Indexed: 12/27/2022]
Abstract
Nargenicin A1, an antibacterial produced by Nocardia sp. CS682 (KCTC 11297BP), demonstrates effective activity against various Gram-positive bacteria. Hence, we attempted to enhance nargenicin A1 production by utilizing the cumulative effect of synthetic biology, metabolic engineering and statistical media optimization strategies. To facilitate the modular assembly of multiple genes for genetic engineering in Nocardia sp. CS682, we constructed a set of multi-monocistronic vectors, pNV18L1 and pNV18L2 containing hybrid promoter (derived from ermE* and promoter region of neo r ), ribosome binding sites (RBS), and restriction sites for cloning, so that each cloned gene was under its own promoter and RBS. The multi-monocistronic vector, pNV18L2 containing transcriptional terminator showed better efficiency in reporter gene assay. Thus, multiple genes involved in the biogenesis of pyrrole moiety (ngnN2, ngnN3, ngnN4, and ngnN5 from Nocardia sp. CS682), glucose utilization (glf and glk from Zymomonas mobilis), and malonyl-CoA synthesis (accA2 and accBE from Streptomyces coelicolor A3 (2)), were cloned in pNV18L2. Further statistical optimization of specific precursors (proline and glucose) and their feeding time led to ~84.9 mg/L nargenicin from Nocardia sp. GAP, which is ~24-fold higher than Nocardia sp. CS682 (without feeding). Furthermore, pikC from Streptomyces venezuelae was expressed to generate Nocardia sp. PikC. Nargenicin A1 acid was characterized as novel derivative of nargenicin A1 produced from Nocardia sp. PikC by mass spectrometry (MS) and nuclear magnetic resonance (NMR) analyses. We also performed comparative analysis of the anticancer and antibacterial activities of nargenicin A1 and nargenicin A1 acid, which showed a reduction in antibacterial potential for nargenicin A1 acid. Thus, the development of an efficient synthetic biological platform provided new avenues for enhancing or structurally diversifying nargenicin A1 by means of pathway designing and engineering.
Collapse
Affiliation(s)
- Dipesh Dhakal
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Amit Kumar Chaudhary
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Jeong Sang Yi
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul, Republic of Korea
| | - Anaya Raj Pokhrel
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Biplav Shrestha
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Prakash Parajuli
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Anil Shrestha
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Tokutaro Yamaguchi
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Hye Jin Jung
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Seung-Young Kim
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute, Seoul National University, Seoul, Republic of Korea
| | - Jae Kyung Sohng
- Department of Life Science and Biochemical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea. .,Department of BT-Convergent Pharmaceutical Engineering, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-si, Chungnam, 31460, Republic of Korea.
| |
Collapse
|
35
|
Fang H, Dong H, Cai T, Zheng P, Li H, Zhang D, Sun J. In Vitro Optimization of Enzymes Involved in Precorrin-2 Synthesis Using Response Surface Methodology. PLoS One 2016; 11:e0151149. [PMID: 26974652 PMCID: PMC4790935 DOI: 10.1371/journal.pone.0151149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/23/2016] [Indexed: 11/19/2022] Open
Abstract
In order to maximize the production of biologically-derived chemicals, kinetic analyses are first necessary for predicting the role of enzyme components and coordinating enzymes in the same reaction system. Precorrin-2 is a key precursor of cobalamin and siroheme synthesis. In this study, we sought to optimize the concentrations of several molecules involved in precorrin-2 synthesis in vitro: porphobilinogen synthase (PBGS), porphobilinogen deaminase (PBGD), uroporphyrinogen III synthase (UROS), and S-adenosyl-l-methionine-dependent urogen III methyltransferase (SUMT). Response surface methodology was applied to develop a kinetic model designed to maximize precorrin-2 productivity. The optimal molar ratios of PBGS, PBGD, UROS, and SUMT were found to be approximately 1:7:7:34, respectively. Maximum precorrin-2 production was achieved at 0.1966 ± 0.0028 μM/min, agreeing with the kinetic model's predicted value of 0.1950 μM/min. The optimal concentrations of the cofactor S-adenosyl-L-methionine (SAM) and substrate 5-aminolevulinic acid (ALA) were also determined to be 200 μM and 5 mM, respectively, in a tandem-enzyme assay. By optimizing the relative concentrations of these enzymes, we were able to minimize the effects of substrate inhibition and feedback inhibition by S-adenosylhomocysteine on SUMT and thereby increase the production of precorrin-2 by approximately five-fold. These results demonstrate the effectiveness of kinetic modeling via response surface methodology for maximizing the production of biologically-derived chemicals.
Collapse
Affiliation(s)
- Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huina Dong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Tao Cai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Haixing Li
- Sino-German Joint Research Institute, Nanchang University, Nanchang, Jiangxi, China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| |
Collapse
|
36
|
Sun X, Shen X, Jain R, Lin Y, Wang J, Sun J, Wang J, Yan Y, Yuan Q. Synthesis of chemicals by metabolic engineering of microbes. Chem Soc Rev 2016; 44:3760-85. [PMID: 25940754 DOI: 10.1039/c5cs00159e] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolic engineering is a powerful tool for the sustainable production of chemicals. Over the years, the exploration of microbial, animal and plant metabolism has generated a wealth of valuable genetic information. The prudent application of this knowledge on cellular metabolism and biochemistry has enabled the construction of novel metabolic pathways that do not exist in nature or enhance existing ones. The hand in hand development of computational technology, protein science and genetic manipulation tools has formed the basis of powerful emerging technologies that make the production of green chemicals and fuels a reality. Microbial production of chemicals is more feasible compared to plant and animal systems, due to simpler genetic make-up and amenable growth rates. Here, we summarize the recent progress in the synthesis of biofuels, value added chemicals, pharmaceuticals and nutraceuticals via metabolic engineering of microbes.
Collapse
Affiliation(s)
- Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 15#, Beisanhuan East Road, Chaoyang District, Beijing 100029, China.
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Synthetic scaffolds for pathway enhancement. Curr Opin Biotechnol 2015; 36:98-106. [DOI: 10.1016/j.copbio.2015.08.009] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 07/31/2015] [Accepted: 08/09/2015] [Indexed: 12/11/2022]
|
38
|
Pröschel M, Detsch R, Boccaccini AR, Sonnewald U. Engineering of Metabolic Pathways by Artificial Enzyme Channels. Front Bioeng Biotechnol 2015; 3:168. [PMID: 26557643 PMCID: PMC4617052 DOI: 10.3389/fbioe.2015.00168] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/06/2015] [Indexed: 11/13/2022] Open
Abstract
Application of industrial enzymes for production of valuable chemical compounds has greatly benefited from recent developments in Systems and Synthetic Biology. Both, in vivo and in vitro systems have been established, allowing conversion of simple into complex compounds. Metabolic engineering in living cells needs to be balanced which is achieved by controlling gene expression levels, translation, scaffolding, compartmentation, and flux control. In vitro applications are often hampered by limited protein stability/half-life and insufficient rates of substrate conversion. To improve stability and catalytic activity, proteins are post-translationally modified and arranged in artificial metabolic channels. Within the review article, we will first discuss the supramolecular organization of enzymes in living systems and second summarize current and future approaches to design artificial metabolic channels by additive manufacturing for the efficient production of desired products.
Collapse
Affiliation(s)
- Marlene Pröschel
- Department of Biology, Biochemistry Division, Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
| | - Rainer Detsch
- Department of Materials Science and Engineering, Institute of Biomaterials, Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
| | - Aldo R Boccaccini
- Department of Materials Science and Engineering, Institute of Biomaterials, Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
| | - Uwe Sonnewald
- Department of Biology, Biochemistry Division, Friedrich-Alexander-University Erlangen-Nuremberg , Erlangen , Germany
| |
Collapse
|
39
|
Parajuli P, Pandey RP, Trang NTH, Chaudhary AK, Sohng JK. Synthetic sugar cassettes for the efficient production of flavonol glycosides in Escherichia coli. Microb Cell Fact 2015; 14:76. [PMID: 26051114 PMCID: PMC4459062 DOI: 10.1186/s12934-015-0261-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/11/2015] [Indexed: 11/23/2022] Open
Abstract
Background A multi-monocistronic synthetic vector was used to assemble multiple genes of a nucleotide diphosphate (NDP)-sugar biosynthetic pathway to construct robust genetic circuits for the production of valuable flavonoid glycosides in Escherichia coli. Characterized functional genes involved in the biosynthesis of uridine diphosphate (UDP)-glucose and thymidine diphosphate (TDP)-rhamnose from various microbial sources along with glucose facilitator diffusion protein (glf) and glucokinase (glk) from Zymomonas mobilis were assembled and overexpressed in a single synthetic multi-monocistronic operon. Results The newly generated NDP-sugars biosynthesis circuits along with regiospecific glycosyltransferases from plants were introduced in E. coli BL21 (DE3) to probe the bioconversion of fisetin, a medicinally important polyphenol produced by various plants. As a result, approximately 1.178 g of fisetin 3-O-glucoside and 1.026 g of fisetin 3-O-rhamnoside were produced in UDP-glucose and TDP-rhamnose biosynthesis systems respectively, after 48 h of incubation in 3 L fermentor while supplementing 0.9 g of fisetin. These yields of fisetin glycosides represent ~99% of bioconversion of exogenously supplemented fisetin. The systems were also found to be highly effective in bio-transforming other flavonols (quercetin, kaempferol, myricetin) into their respective glycosides, achieving over 95% substrate conversion. Conclusion The construction of a synthetic expression vector for bacterial cell factory followed by subsequent re-direction of metabolic flux towards desirable products have always been revolutionized the biotechnological processes and technologies. This multi-monocistronic synthetic vector in a microbial platform is customizable to defined task and would certainly be useful for applications in producing and modifying such therapeutically valued plant secondary metabolites. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0261-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Prakash Parajuli
- Department of BT-Convergent Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-Si, Chungnam, 336-708, Republic of Korea.
| | - Ramesh Prasad Pandey
- Department of BT-Convergent Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-Si, Chungnam, 336-708, Republic of Korea.
| | - Nguyen Thi Huyen Trang
- Department of BT-Convergent Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-Si, Chungnam, 336-708, Republic of Korea.
| | - Amit Kumar Chaudhary
- Department of BT-Convergent Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-Si, Chungnam, 336-708, Republic of Korea.
| | - Jae Kyung Sohng
- Department of BT-Convergent Pharmaceutical Engineering, Institute of Biomolecule Reconstruction, Sun Moon University, 70 Sunmoon-ro 221, Tangjeong-myeon, Asan-Si, Chungnam, 336-708, Republic of Korea.
| |
Collapse
|
40
|
Lieder S, Nikel PI, de Lorenzo V, Takors R. Genome reduction boosts heterologous gene expression in Pseudomonas putida. Microb Cell Fact 2015; 14:23. [PMID: 25890048 PMCID: PMC4352270 DOI: 10.1186/s12934-015-0207-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 02/11/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The implementation of novel platform organisms to be used as microbial cell factories in industrial applications is currently the subject of intense research. Ongoing efforts include the adoption of Pseudomonas putida KT2440 variants with a reduced genome as the functional chassis for biotechnological purposes. In these strains, dispensable functions removed include flagellar motility (1.1% of the genome) and a number of open reading frames expected to improve genotypic and phenotypic stability of the cells upon deletion (3.2% of the genome). RESULTS In this study, two previously constructed multiple-deletion P. putida strains were systematically evaluated as microbial cell factories for heterologous protein production and compared to the parental bacterium (strain KT2440) with regards to several industrially-relevant physiological traits. Energetic parameters were quantified at different controlled growth rates in continuous cultivations and both strains had a higher adenosine triphosphate content, increased adenylate energy charges, and diminished maintenance demands than the wild-type strain. Under all the conditions tested the mutants also grew faster, had enhanced biomass yields and showed higher viability, and displayed increased plasmid stability than the parental strain. In addition to small-scale shaken-flask cultivations, the performance of the genome-streamlined strains was evaluated in larger scale bioreactor batch cultivations taking a step towards industrial growth conditions. When the production of the green fluorescent protein (used as a model heterologous protein) was assessed in these cultures, the mutants reached a recombinant protein yield with respect to biomass up to 40% higher than that of P. putida KT2440. CONCLUSIONS The two streamlined-genome derivatives of P. putida KT2440 outcompeted the parental strain in every industrially-relevant trait assessed, particularly under the working conditions of a bioreactor. Our results demonstrate that these genome-streamlined bacteria are not only robust microbial cell factories on their own, but also a promising foundation for further biotechnological applications.
Collapse
Affiliation(s)
- Sarah Lieder
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
| | - Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain.
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), C/Darwin 3, 28049, Madrid, Spain.
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
| |
Collapse
|
41
|
Pfleger BF, Gossing M, Nielsen J. Metabolic engineering strategies for microbial synthesis of oleochemicals. Metab Eng 2015; 29:1-11. [PMID: 25662836 DOI: 10.1016/j.ymben.2015.01.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/27/2015] [Accepted: 01/28/2015] [Indexed: 11/30/2022]
Abstract
Microbial synthesis of oleochemicals has advanced significantly in the last decade. Microbes have been engineered to convert renewable substrates to a wide range of molecules that are ordinarily made from plant oils. This approach is attractive because it can reduce a motivation for converting tropical rainforest into farmland while simultaneously enabling access to molecules that are currently expensive to produce from oil crops. In the last decade, enzymes responsible for producing oleochemicals in nature have been identified, strategies to circumvent native regulation have been developed, and high yielding strains have been designed, built, and successfully demonstrated. This review will describe the metabolic pathways that lead to the diverse molecular features found in natural oleochemicals, highlight successful metabolic engineering strategies, and comment on areas where future work could further advance the field.
Collapse
Affiliation(s)
- Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States.
| | - Michael Gossing
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| |
Collapse
|
42
|
Characterizing Synthetic Biology Through Its Novel and Enhanced Functionalities. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
|
43
|
Martínez-García E, Nikel PI, Aparicio T, de Lorenzo V. Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression. Microb Cell Fact 2014; 13:159. [PMID: 25384394 PMCID: PMC4230525 DOI: 10.1186/s12934-014-0159-3] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Accepted: 10/27/2014] [Indexed: 11/10/2022] Open
Abstract
Background Because of its adaptability to sites polluted with toxic chemicals, the model soil bacterium Pseudomonas putida is naturally endowed with a number of metabolic and stress-endurance qualities which have considerable value for hosting energy-demanding and redox reactions thereof. The growing body of knowledge on P. putida strain KT2440 has been exploited for the rational design of a derivative strain in which the genome has been heavily edited in order to construct a robust microbial cell factory. Results Eleven non-adjacent genomic deletions, which span 300 genes (i.e., 4.3% of the entire P. putida KT2440 genome), were eliminated; thereby enhancing desirable traits and eliminating attributes which are detrimental in an expression host. Since ATP and NAD(P)H availability – as well as genetic instability, are generally considered to be major bottlenecks for the performance of platform strains, a suite of functions that drain high-energy phosphate from the cells and/or consume NAD(P)H were targeted in particular, the whole flagellar machinery. Four prophages, two transposons, and three components of DNA restriction-modification systems were eliminated as well. The resulting strain (P. putida EM383) displayed growth properties (i.e., lag times, biomass yield, and specific growth rates) clearly superior to the precursor wild-type strain KT2440. Furthermore, it tolerated endogenous oxidative stress, acquired and replicated exogenous DNA, and survived better in stationary phase. The performance of a bi-cistronic GFP-LuxCDABE reporter system as a proxy of combined metabolic vitality, revealed that the deletions in P. putida strain EM383 brought about an increase of >50% in the overall physiological vigour. Conclusion The rationally modified P. putida strain allowed for the better functional expression of implanted genes by directly improving the metabolic currency that sustains the gene expression flow, instead of resorting to the classical genetic approaches (e.g., increasing the promoter strength in the DNA constructs of interest). Electronic supplementary material The online version of this article (doi:10.1186/s12934-014-0159-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Esteban Martínez-García
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Tomás Aparicio
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| |
Collapse
|
44
|
Martínez-García E, Nikel PI, Aparicio T, de Lorenzo V. Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression. Microb Cell Fact 2014. [PMID: 25384394 DOI: 10.1186/s12934-014-0159-3.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Because of its adaptability to sites polluted with toxic chemicals, the model soil bacterium Pseudomonas putida is naturally endowed with a number of metabolic and stress-endurance qualities which have considerable value for hosting energy-demanding and redox reactions thereof. The growing body of knowledge on P. putida strain KT2440 has been exploited for the rational design of a derivative strain in which the genome has been heavily edited in order to construct a robust microbial cell factory. RESULTS Eleven non-adjacent genomic deletions, which span 300 genes (i.e., 4.3% of the entire P. putida KT2440 genome), were eliminated; thereby enhancing desirable traits and eliminating attributes which are detrimental in an expression host. Since ATP and NAD(P)H availability - as well as genetic instability, are generally considered to be major bottlenecks for the performance of platform strains, a suite of functions that drain high-energy phosphate from the cells and/or consume NAD(P)H were targeted in particular, the whole flagellar machinery. Four prophages, two transposons, and three components of DNA restriction-modification systems were eliminated as well. The resulting strain (P. putida EM383) displayed growth properties (i.e., lag times, biomass yield, and specific growth rates) clearly superior to the precursor wild-type strain KT2440. Furthermore, it tolerated endogenous oxidative stress, acquired and replicated exogenous DNA, and survived better in stationary phase. The performance of a bi-cistronic GFP-LuxCDABE reporter system as a proxy of combined metabolic vitality, revealed that the deletions in P. putida strain EM383 brought about an increase of >50% in the overall physiological vigour. CONCLUSION The rationally modified P. putida strain allowed for the better functional expression of implanted genes by directly improving the metabolic currency that sustains the gene expression flow, instead of resorting to the classical genetic approaches (e.g., increasing the promoter strength in the DNA constructs of interest).
Collapse
Affiliation(s)
- Esteban Martínez-García
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Tomás Aparicio
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, 28049, Madrid, Spain.
| |
Collapse
|
45
|
Liang Q, Qi Q. From a co-production design to an integrated single-cell biorefinery. Biotechnol Adv 2014; 32:1328-1335. [DOI: 10.1016/j.biotechadv.2014.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 07/23/2014] [Accepted: 08/17/2014] [Indexed: 10/24/2022]
|
46
|
Engineering redox balance through cofactor systems. Trends Biotechnol 2014; 32:337-43. [DOI: 10.1016/j.tibtech.2014.04.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 03/26/2014] [Accepted: 04/02/2014] [Indexed: 12/12/2022]
|
47
|
Su H, Zhao Y, Zhao H, Wang M, Li Q, Jiang J, Lu Q. Identification and assessment of the effects of yeast decarboxylases expressed in Escherichia coli
for producing higher alcohols. J Appl Microbiol 2014; 117:126-38. [DOI: 10.1111/jam.12510] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/05/2014] [Accepted: 03/21/2014] [Indexed: 01/15/2023]
Affiliation(s)
- H. Su
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Y. Zhao
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - H. Zhao
- Bioenergy Laboratory; Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu China
| | - M. Wang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Q. Li
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - J. Jiang
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| | - Q. Lu
- Key Laboratory of Bio-resources and Eco-environment of Ministry of Education; College of Life Sciences; Sichuan University; Chengdu China
| |
Collapse
|
48
|
Brück T, Kourist R, Loll B. Production of Macrocyclic Sesqui- and Diterpenes in Heterologous Microbial Hosts: A Systems Approach to Harness Nature’s Molecular Diversity. ChemCatChem 2014. [DOI: 10.1002/cctc.201300733] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
49
|
Yang JE, Choi SY, Shin JH, Park SJ, Lee SY. Microbial production of lactate-containing polyesters. Microb Biotechnol 2013; 6:621-36. [PMID: 23718266 PMCID: PMC3815930 DOI: 10.1111/1751-7915.12066] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 04/19/2013] [Accepted: 04/22/2013] [Indexed: 12/31/2022] Open
Abstract
Due to our increasing concerns on environmental problems and limited fossil resources, biobased production of chemicals and materials through biorefinery has been attracting much attention. Optimization of the metabolic performance of microorganisms, the key biocatalysts for the efficient production of the desired target bioproducts, has been achieved by metabolic engineering. Metabolic engineering allowed more efficient production of polyhydroxyalkanoates, a family of microbial polyesters. More recently, non-natural polyesters containing lactate as a monomer have also been produced by one-step fermentation of engineered bacteria. Systems metabolic engineering integrating traditional metabolic engineering with systems biology, synthetic biology, protein/enzyme engineering through directed evolution and structural design, and evolutionary engineering, enabled microorganisms to efficiently produce natural and non-natural products. Here, we review the strategies for the metabolic engineering of microorganisms for the in vivo biosynthesis of lactate-containing polyesters and for the optimization of whole cell metabolism to efficiently produce lactate-containing polyesters. Also, major problems to be solved to further enhance the production of lactate-containing polyesters are discussed.
Collapse
Affiliation(s)
- Jung Eun Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Institute for the BioCentury, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Institute for the BioCentury, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
| | - Jae Ho Shin
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Institute for the BioCentury, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
| | - Si Jae Park
- Department of Environmental Engineering and Energy (Undergraduate program), Myongji UniversitySan 38-2, Nam-dong, Cheoin-gu, Yongin-si, Gyeonggido, 449-728, Korea
- Department of Energy Science and Technology (Graduate program), Myongji UniversitySan 38-2, Nam-dong, Cheoin-gu, Yongin-si, Gyeonggido, 449-728, Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program), Center for Systems and Synthetic Biotechnology, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Institute for the BioCentury, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Department of Bio and Brain Engineering, Department of Biological Sciences, BioProcess Engineering Research Center, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
- Bioinformatics Research Center, KAIST291 Daehak-ro, Yuseong-gu, Daejeon, 305-701, Korea
| |
Collapse
|
50
|
Gerard MF, Stegmayer G, Milone DH. An evolutionary approach for searching metabolic pathways. Comput Biol Med 2013; 43:1704-12. [DOI: 10.1016/j.compbiomed.2013.08.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 08/18/2013] [Accepted: 08/21/2013] [Indexed: 11/26/2022]
|