1
|
Tan W, Miao Q, Jia X, Liu Y, Li S, Yang D. Research Progress on the Assembly of Large DNA Fragments. Chembiochem 2024; 25:e202400054. [PMID: 38477700 DOI: 10.1002/cbic.202400054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Synthetic biology, a newly and rapidly developing interdisciplinary field, has demonstrated increasing potential for extensive applications in the wide areas of biomedicine, biofuels, and novel materials. DNA assembly is a key enabling technology of synthetic biology and a central point for realizing fully synthetic artificial life. While the assembly of small DNA fragments has been successfully commercialized, the assembly of large DNA fragments remains a challenge due to their high molecular weight and susceptibility to breakage. This article provides an overview of the development and current state of DNA assembly technology, with a focus on recent advancements in the assembly of large DNA fragments in Escherichia coli, Bacillus subtilis, and Saccharomyces cerevisiae. In particular, the methods and challenges associated with the assembly of large DNA fragment in different hosts are highlighted. The advancements in DNA assembly have the potential to facilitate the construction of customized genomes, giving us the ability to modify cellular functions and even create artificial life. It is also contributing to our ability to understand, predict, and manipulate living organisms.
Collapse
Affiliation(s)
- Wei Tan
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Qing Miao
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Xuemei Jia
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Ying Liu
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, P. R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, 315201, P. R. China
| |
Collapse
|
2
|
Raman J, Ko YJ, Kim JS, Kim DH, Kim SJ. Overproduction of Xanthophyll Pigment in Flavobacterium sp. JSWR-1 under Optimized Culture Conditions. J Microbiol Biotechnol 2024; 34:710-724. [PMID: 38044702 PMCID: PMC11016774 DOI: 10.4014/jmb.2310.10034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/14/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023]
Abstract
Flavobacterium can synthesize xanthophyll, particularly the pigment zeaxanthin, which has significant economic value in nutrition and pharmaceuticals. Recently, the use of carotenoid biosynthesis by bacteria and yeast fermentation technology has shown to be very efficient and offers significant advantages in large-scale production, cost-effectiveness, and safety. In the present study, JSWR-1 strain capable of producing xanthophyll pigment was isolated from a freshwater reservoir in Wanju-gun, Republic of Korea. Based on the morphological, physiological, and molecular characteristics, JSWR-1 classified as belonging to the Flavobacterium species. The bacterium is strictly aerobic, Gram-negative, rod-shaped, and psychrophilic. The completed genome sequence of the strain Flavobacterium sp. JSWR-1 is predicted to be a single circular 3,425,829-bp chromosome with a G+C content of 35.2% and 2,941 protein-coding genes. The optimization of carotenoid production was achieved by small-scale cultivation, resulting in zeaxanthin being identified as the predominant carotenoid pigment. The enhancement of zeaxanthin biosynthesis by applying different light-irradiation, variations in pH and temperature, and adding carbon and nitrogen supplies to the growth medium. A significant increase in intracellular zeaxanthin concentrations was also recorded during fed-batch fermentation achieving a maximum of 16.69 ± 0.71 mg/l, corresponding to a product yield of 4.05 ± 0.15 mg zeaxanthin per gram cell dry weight. Batch and fed-batch culture extracts exhibit significant antioxidant activity. The results demonstrated that the JSWR-1 strain can potentially serve as a source for zeaxanthin biosynthesis.
Collapse
Affiliation(s)
- Jegadeesh Raman
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Young-Joon Ko
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Jeong-Seon Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Da-Hye Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| | - Soo-Jin Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do 55365, Republic of Korea
| |
Collapse
|
3
|
Bouin A, Zhang C, Lindley ND, Truan G, Lautier T. Exploring linker's sequence diversity to fuse carotene cyclase and hydroxylase for zeaxanthin biosynthesis. Metab Eng Commun 2023; 16:e00222. [PMID: 37168436 PMCID: PMC10165439 DOI: 10.1016/j.mec.2023.e00222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/16/2023] [Indexed: 05/13/2023] Open
Abstract
Fusion of catalytic domains can accelerate cascade reactions by bringing enzymes in close proximity. However, the design of a protein fusion and the choice of a linker are often challenging and lack of guidance. To determine the impact of linker parameters on fusion proteins, a library of linkers featuring various lengths, secondary structures, extensions and hydrophobicities was designed. Linkers were used to fuse the lycopene cyclase (crtY) and β-carotene hydroxylase (crtZ) from Pantoea ananatis to create fusion proteins to produce zeaxanthin. The fusion efficiency was assessed by comparing the carotenoids content in a carotenoid-producer Escherichia coli strain. It was shown that in addition to the orientation of the enzymes and the size of the linker, the first amino acid of the linker is also a key factor in determining the efficiency of a protein fusion. The wide range of sequence diversity in our linker library enables the fine tuning of protein fusion and this approach can be easily transferred to other enzyme couples.
Collapse
Affiliation(s)
- Aurélie Bouin
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Congqiang Zhang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore
- Corresponding author.
| | - Nic D. Lindley
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Gilles Truan
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Corresponding author.
| | - Thomas Lautier
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- CNRS@CREATE, 1 Create Way, #08-01 Create Tower, 138602, Singapore
- Corresponding author. Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore.
| |
Collapse
|
4
|
Wang N, Peng H, Yang C, Guo W, Wang M, Li G, Liu D. Metabolic Engineering of Model Microorganisms for the Production of Xanthophyll. Microorganisms 2023; 11:1252. [PMID: 37317226 DOI: 10.3390/microorganisms11051252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/19/2023] [Accepted: 05/06/2023] [Indexed: 06/16/2023] Open
Abstract
Xanthophyll is an oxidated version of carotenoid. It presents significant value to the pharmaceutical, food, and cosmetic industries due to its specific antioxidant activity and variety of colors. Chemical processing and conventional extraction from natural organisms are still the main sources of xanthophyll. However, the current industrial production model can no longer meet the demand for human health care, reducing petrochemical energy consumption and green sustainable development. With the swift development of genetic metabolic engineering, xanthophyll synthesis by the metabolic engineering of model microorganisms shows great application potential. At present, compared to carotenes such as lycopene and β-carotene, xanthophyll has a relatively low production in engineering microorganisms due to its stronger inherent antioxidation, relatively high polarity, and longer metabolic pathway. This review comprehensively summarized the progress in xanthophyll synthesis by the metabolic engineering of model microorganisms, described strategies to improve xanthophyll production in detail, and proposed the current challenges and future efforts needed to build commercialized xanthophyll-producing microorganisms.
Collapse
Affiliation(s)
- Nan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huakang Peng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Caifeng Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenfang Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mengqi Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Gangqiang Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dehu Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| |
Collapse
|
5
|
Wang L, Deng Y, Peng R, Gao J, Li Z, Zhang W, Xu J, Wang B, Wang Y, Han H, Fu X, Tian Y, Yao Q. Metabolic engineering for the biosynthesis of bis-indolylquinone terrequinone A in Escherichia coli from L-tryptophan and prenol. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:34. [PMID: 36859334 PMCID: PMC9979454 DOI: 10.1186/s13068-023-02284-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Terrequinone A is a bis-indolylquinone natural product with antitumor activity. Due to its unique asymmetric quinone core structure and multiple functional groups, biosynthesis is more efficient and environmentally friendly than traditional chemical synthesis. Currently, most bis-indolylquinones are obtained by direct extraction from fungi or by chemical synthesis. By focusing on the biosynthesis of terrequinone A, we hope to explore the way to synthesize bis-indolylquinones de novo using Escherichia coli as a cell factory. RESULTS In this study, a terrequinone A synthesis pathway containing the tdiA-tdiE genes was constructed into Escherichia coli and activated by a phosphopantetheinyl transferase gene sfp, enabling the strain to synthesize 1.54 mg/L of terrequinone A. Subsequently, a two-step isopentenol utilization pathway was introduced to enhance the supply of endogenous dimethylallyl diphosphate (DMAPP) in E. coli, increasing the level of terrequinone A to 20.1 mg/L. By adjusting the L-tryptophan (L-Trp)/prenol ratio, the major product could be changed from ochrindole D to terrequinone A, and the content of terrequinone A reached the highest 106.3 mg/L under the optimized culture conditions. Metabolic analysis of L-Trp indicated that the conversion of large amounts of L-Trp to indole was an important factor preventing the further improvement of terrequinone A yield. CONCLUSIONS A comprehensive approach was adopted and terrequinone A was successfully synthesized from low-cost L-Trp and prenol in E. coli. This study provides a metabolic engineering strategy for the efficient synthesis of terrequinone A and other similar bis-indolylquinones with asymmetric quinone cores. In addition, this is the first report on the de novo biosyhthesis of terrequinone A in an engineered strain.
Collapse
Affiliation(s)
- Lijuan Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Yongdong Deng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Rihe Peng
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Jianjie Gao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Zhenjun Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Wenhui Zhang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Jing Xu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Bo Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Yu Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Hongjuan Han
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Xiaoyan Fu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Yongsheng Tian
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China.
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China.
| | - Quanhong Yao
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, 2901 Beidi Road, Shanghai, China.
- Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Shanghai, China.
| |
Collapse
|
6
|
Abioye J, Lawson-Williams M, Lecanda A, Calhoon B, McQue AL, Colloms SD, Stark WM, Olorunniji FJ. High fidelity one-pot DNA assembly using orthogonal serine integrases. Biotechnol J 2023; 18:e2200411. [PMID: 36504358 DOI: 10.1002/biot.202200411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/08/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND Large serine integrases (LSIs, derived from temperate phages) have been adapted for use in a multipart DNA assembly process in vitro, called serine integrase recombinational assembly (SIRA). The versatility, efficiency, and fidelity of SIRA is limited by lack of a sufficient number of LSIs whose activities have been characterized in vitro. METHODS AND MAJOR RESULTS In this report, we compared the activities in vitro of 10 orthogonal LSIs to explore their suitability for multiplex SIRA reactions. We found that Bxb1, ϕR4, and TG1 integrases were the most active among the set we studied, but several others were also usable. As proof of principle, we demonstrated high-efficiency one-pot assembly of six DNA fragments (made by PCR) into a 7.5 kb plasmid that expresses the enzymes of the β-carotenoid pathway in Escherichia coli, using six different LSIs. We further showed that a combined approach using a few highly active LSIs, each acting on multiple pairs of att sites with distinct central dinucleotides, can be used to scale up "poly-part" gene assembly and editing. CONCLUSIONS AND IMPLICATIONS We conclude that use of multiple orthogonal integrases may be the most predictable, efficient, and programmable approach for SIRA and other in vitro applications.
Collapse
Affiliation(s)
- Jumai Abioye
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Makeba Lawson-Williams
- School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Liverpool, UK
| | - Alicia Lecanda
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Brecken Calhoon
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Arlene L McQue
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Sean D Colloms
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - W Marshall Stark
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Femi J Olorunniji
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
- School of Pharmacy and Biomolecular Sciences, Faculty of Science, Liverpool John Moores University, Liverpool, UK
| |
Collapse
|
7
|
Bacterial Pigments and Their Multifaceted Roles in Contemporary Biotechnology and Pharmacological Applications. Microorganisms 2023; 11:microorganisms11030614. [PMID: 36985186 PMCID: PMC10053885 DOI: 10.3390/microorganisms11030614] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/05/2023] Open
Abstract
Synthetic dyes and colourants have been the mainstay of the pigment industry for decades. Researchers are eager to find a more environment friendly and non-toxic substitute because these synthetic dyes have a negative impact on the environment and people’s health. Microbial pigments might be an alternative to synthetic pigments. Microbial pigments are categorized as secondary metabolites and are mainly produced due to impaired metabolism under stressful conditions. These pigments have vibrant shades and possess nutritional and therapeutic properties compared to synthetic pigment. Microbial pigments are now widely used within the pharmaceuticals, food, paints, and textile industries. The pharmaceutical industries currently use bacterial pigments as a medicine alternative for cancer and many other bacterial infections. Their growing popularity is a result of their low cost, biodegradable, non-carcinogenic, and environmentally beneficial attributes. This audit article has made an effort to take an in-depth look into the existing uses of bacterial pigments in the food and pharmaceutical industries and project their potential future applications.
Collapse
|
8
|
Selection for Translational Efficiency in Genes Associated with Alphaproteobacterial Gene Transfer Agents. mSystems 2022; 7:e0089222. [PMID: 36374047 PMCID: PMC9765227 DOI: 10.1128/msystems.00892-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Gene transfer agents (GTAs) are virus-like elements that are encoded by some bacterial and archaeal genomes. The production of GTAs can be induced by carbon depletion and results in host lysis and the release of virus-like particles that contain mostly random fragments of the host DNA. The remaining members of a GTA-producing population act as GTA recipients by producing proteins needed for GTA-mediated DNA acquisition. Here, we detected a codon usage bias toward codons with more readily available tRNAs in the RcGTA-like GTA genes of alphaproteobacterial genomes. Such bias likely improves the translational efficacy during GTA gene expression. While the strength of codon usage bias fluctuates substantially among individual GTA genes and across taxonomic groups, it is especially pronounced in Sphingomonadales, whose members are known to inhabit nutrient-depleted environments. By screening genomes for gene families with trends in codon usage biases similar to those in GTA genes, we found a gene that likely encodes head completion protein in some GTAs where it appeared missing, and 13 genes previously not implicated in the GTA life cycle. The latter genes are involved in various molecular processes, including the homologous recombination and transport of scarce organic matter. Our findings provide insights into the role of selection for translational efficiency in the evolution of GTA genes and outline genes that are potentially involved in the previously hypothesized integration of GTA-delivered DNA into the host genome. IMPORTANCE Horizontal gene transfer (HGT) is a fundamental process that drives evolution of microorganisms. HGT can result in a rapid dissemination of beneficial genes within and among microbial communities and can be achieved via multiple mechanisms. One peculiar HGT mechanism involves viruses "domesticated" by some bacteria and archaea (their hosts). These so-called gene transfer agents (GTAs) are encoded in hosts' genomes, produced under starvation conditions, and cannot propagate themselves as viruses. We show that GTA genes are under selection to improve the efficiency of their translation when the host activates GTA production. The selection is especially pronounced in bacteria that occupy nutrient-depleted environments. Intriguingly, several genes involved in incorporation of DNA into a genome are under similar selection pressure, suggesting that they may facilitate the integration of GTA-delivered DNA into the host genome. Our findings underscore the potential importance of GTAs as a mechanism of HGT under nutrient-limited conditions, which are widespread in microbial habitats.
Collapse
|
9
|
Carotenoids in Drug Discovery and Medicine: Pathways and Molecular Targets Implicated in Human Diseases. Molecules 2022; 27:molecules27186005. [PMID: 36144741 PMCID: PMC9503763 DOI: 10.3390/molecules27186005] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Carotenoids are isoprenoid-derived natural products produced in plants, algae, fungi, and photosynthetic bacteria. Most animals cannot synthesize carotenoids because the biosynthetic machinery to create carotenoids de novo is absent in animals, except arthropods. Carotenoids are biosynthesized from two C20 geranylgeranyl pyrophosphate (GGPP) molecules made from isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) via the methylerythritol 4-phosphate (MEP) route. Carotenoids can be extracted by a variety of methods, including maceration, Soxhlet extraction, supercritical fluid extraction (SFE), microwave-assisted extraction (MAE), accelerated solvent extraction (ASE), ultrasound-assisted extraction (UAE), pulsed electric field (PEF)-assisted extraction, and enzyme-assisted extraction (EAE). Carotenoids have been reported to exert various biochemical actions, including the inhibition of the Akt/mTOR, Bcl-2, SAPK/JNK, JAK/STAT, MAPK, Nrf2/Keap1, and NF-κB signaling pathways and the ability to increase cholesterol efflux to HDL. Carotenoids are absorbed in the intestine. A handful of carotenoids and carotenoid-based compounds are in clinical trials, while some are currently used as medicines. The application of metabolic engineering techniques for carotenoid production, whole-genome sequencing, and the use of plants as cell factories to produce specialty carotenoids presents a promising future for carotenoid research. In this review, we discussed the biosynthesis and extraction of carotenoids, the roles of carotenoids in human health, the metabolism of carotenoids, and carotenoids as a source of drugs and supplements.
Collapse
|
10
|
Steven R, Humaira Z, Natanael Y, Dwivany FM, Trinugroho JP, Dwijayanti A, Kristianti T, Tallei TE, Emran TB, Jeon H, Alhumaydhi FA, Radjasa OK, Kim B. Marine Microbial-Derived Resource Exploration: Uncovering the Hidden Potential of Marine Carotenoids. Mar Drugs 2022; 20:352. [PMID: 35736155 PMCID: PMC9229179 DOI: 10.3390/md20060352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 12/04/2022] Open
Abstract
Microbes in marine ecosystems are known to produce secondary metabolites. One of which are carotenoids, which have numerous industrial applications, hence their demand will continue to grow. This review highlights the recent research on natural carotenoids produced by marine microorganisms. We discuss the most recent screening approaches for discovering carotenoids, using in vitro methods such as culture-dependent and culture-independent screening, as well as in silico methods, using secondary metabolite Biosynthetic Gene Clusters (smBGCs), which involves the use of various rule-based and machine-learning-based bioinformatics tools. Following that, various carotenoids are addressed, along with their biological activities and metabolic processes involved in carotenoids biosynthesis. Finally, we cover the application of carotenoids in health and pharmaceutical industries, current carotenoids production system, and potential use of synthetic biology in carotenoids production.
Collapse
Affiliation(s)
- Ray Steven
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung 40132, Indonesia; (R.S.); (Z.H.); (Y.N.)
| | - Zalfa Humaira
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung 40132, Indonesia; (R.S.); (Z.H.); (Y.N.)
| | - Yosua Natanael
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung 40132, Indonesia; (R.S.); (Z.H.); (Y.N.)
| | - Fenny M. Dwivany
- Institut Teknologi Bandung, School of Life Sciences and Technology, Bandung 40132, Indonesia; (R.S.); (Z.H.); (Y.N.)
| | - Joko P. Trinugroho
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, UK;
| | - Ari Dwijayanti
- CNRS@CREATE Ltd., 1 Create Way, #08-01 Create Tower, Singapore 138602, Singapore;
| | | | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Heewon Jeon
- Department of Pathology, College of Korean Medicine, Kyung Hee University, 1-5 Hoegidong, Seoul 02447, Korea;
| | - Fahad A. Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 52571, Saudi Arabia;
| | - Ocky Karna Radjasa
- Oceanography Research Center, The Earth Sciences and Maritime Research Organization, National Research and Innovation Agency, North Jakarta 14430, Indonesia
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, 1-5 Hoegidong, Seoul 02447, Korea;
| |
Collapse
|
11
|
Toya Y, Hirono-Hara Y, Hirayama H, Kamata K, Tanaka R, Sano M, Kitamura S, Otsuka K, Abe-Yoshizumi R, Tsunoda SP, Kikukawa H, Kandori H, Shimizu H, Matsuda F, Ishii J, Hara KY. Optogenetic reprogramming of carbon metabolism using light-powering microbial proton pump systems. Metab Eng 2022; 72:227-236. [PMID: 35346842 DOI: 10.1016/j.ymben.2022.03.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/06/2022] [Accepted: 03/23/2022] [Indexed: 12/27/2022]
Abstract
In microbial fermentative production, ATP regeneration, while crucial for cellular processes, conflicts with efficient target chemical production because ATP regeneration exhausts essential carbon sources also required for target chemical biosynthesis. To wrestle with this dilemma, we harnessed the power of microbial rhodopsins with light-driven proton pumping activity to supplement with ATP, thereby facilitating the bioproduction of various chemicals. We first demonstrated a photo-driven ATP supply and redistribution of metabolic carbon flows to target chemical synthesis by installing already-known delta rhodopsin (dR) in Escherichia coli. In addition, we identified novel rhodopsins with higher proton pumping activities than dR, and created an engineered cell for in vivo self-supply of the rhodopsin-activator, all-trans-retinal. Our concept exploiting the light-powering ATP supplier offers a potential increase in carbon use efficiency for microbial productions through metabolic reprogramming.
Collapse
Affiliation(s)
- Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoko Hirono-Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hidenobu Hirayama
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kentaro Kamata
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryo Tanaka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Mikoto Sano
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kensuke Otsuka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Satoshi P Tsunoda
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Kikukawa
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi, 466-8555, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Jun Ishii
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, Hyogo, 657-8501, Japan
| | - Kiyotaka Y Hara
- Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan; Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, 422-8526, Japan.
| |
Collapse
|
12
|
Casas A, Bultelle M, Motraghi C, Kitney R. PASIV: A Pooled Approach-Based Workflow to Overcome Toxicity-Induced Design of Experiments Failures and Inefficiencies. ACS Synth Biol 2022; 11:1272-1291. [PMID: 35261238 PMCID: PMC8938949 DOI: 10.1021/acssynbio.1c00562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
We present here a
newly developed workflow—which we have
called PASIV—designed to provide a solution to a practical
problem with design of experiments (DoE) methodology: i.e., what can
be done if the scoping phase of the DoE cycle is severely hampered
by burden and toxicity issues (caused by either the metabolite or
an intermediary), making it unreliable or impossible to proceed to
the screening phase? PASIV—standing for pooled approach, screening,
identification, and visualization—was designed so the (viable)
region of interest can be made to appear through an interplay between
biology and software. This was achieved by combining multiplex construction
in a pooled approach (one-pot reaction) with a viability assay and
with a range of bioinformatics tools (including a novel construct
matching tool). PASIV was tested on the exemplar of the lycopene pathway—under
stressful constitutive expression—yielding a region of interest
with comparatively stronger producers.
Collapse
Affiliation(s)
- Alexis Casas
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Matthieu Bultelle
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Charles Motraghi
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| | - Richard Kitney
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, United Kingdom
| |
Collapse
|
13
|
Nishi T, Ito Y, Nakamura Y, Yamaji T, Hashiba N, Tamai M, Yasohara Y, Ishii J, Kondo A. One-Step In Vivo Assembly of Multiple DNA Fragments and Genomic Integration in Komagataella phaffii. ACS Synth Biol 2022; 11:644-654. [PMID: 35094517 DOI: 10.1021/acssynbio.1c00302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The methylotrophic yeast species Komagataella phaffii (synonym: Pichia pastoris) is widely used as a host for recombinant protein production. Although several genetic engineering techniques are being employed on K. phaffii, advanced methods such as in vivo DNA assembly in this yeast species are required for synthetic biology applications. In this study, we established a technique for accomplishing one-step in vivo assembly of multiple DNA fragments and genomic integration in K. phaffii. To concurrently achieve an accurate multiple DNA assembly and a high-efficient integration into the target genomic locus in vivo, a K. phaffii strain, lacking a non-homologous end joining-related protein, DNA ligase IV (Dnl4p), that has been reported to improve gene targeting efficiency by homologous recombination, was used. Using green fluorescent protein along with the lycopene biosynthesis, we showed that our method that included a Dnl4p-defective strain permits direct and easy engineering of K. phaffii strains.
Collapse
Affiliation(s)
- Teruyuki Nishi
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Biotechnology Research Laboratories, Pharma & Supplemental Nutrition Solutions Vehicle, Kaneka Corporation, Takasago 676-8688, Japan
| | - Yoichiro Ito
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Yasuyuki Nakamura
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Taiki Yamaji
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe 650-0047, Japan
| | - Noriko Hashiba
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe 650-0047, Japan
| | - Masaya Tamai
- Technology Research Association of Highly Efficient Gene Design (TRAHED), Kobe 650-0047, Japan
| | - Yoshihiko Yasohara
- Biotechnology Research Laboratories, Pharma & Supplemental Nutrition Solutions Vehicle, Kaneka Corporation, Takasago 676-8688, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe 657-8501, Japan
- Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan
| |
Collapse
|
14
|
Casas A, Bultelle M, Motraghi C, Kitney R. Removing the Bottleneck: Introducing cMatch - A Lightweight Tool for Construct-Matching in Synthetic Biology. Front Bioeng Biotechnol 2022; 9:785131. [PMID: 35083201 PMCID: PMC8784771 DOI: 10.3389/fbioe.2021.785131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 12/14/2021] [Indexed: 11/30/2022] Open
Abstract
We present a software tool, called cMatch, to reconstruct and identify synthetic genetic constructs from their sequences, or a set of sub-sequences—based on two practical pieces of information: their modular structure, and libraries of components. Although developed for combinatorial pathway engineering problems and addressing their quality control (QC) bottleneck, cMatch is not restricted to these applications. QC takes place post assembly, transformation and growth. It has a simple goal, to verify that the genetic material contained in a cell matches what was intended to be built - and when it is not the case, to locate the discrepancies and estimate their severity. In terms of reproducibility/reliability, the QC step is crucial. Failure at this step requires repetition of the construction and/or sequencing steps. When performed manually or semi-manually QC is an extremely time-consuming, error prone process, which scales very poorly with the number of constructs and their complexity. To make QC frictionless and more reliable, cMatch performs an operation we have called “construct-matching” and automates it. Construct-matching is more thorough than simple sequence-matching, as it matches at the functional level-and quantifies the matching at the individual component level and across the whole construct. Two algorithms (called CM_1 and CM_2) are presented. They differ according to the nature of their inputs. CM_1 is the core algorithm for construct-matching and is to be used when input sequences are long enough to cover constructs in their entirety (e.g., obtained with methods such as next generation sequencing). CM_2 is an extension designed to deal with shorter data (e.g., obtained with Sanger sequencing), and that need recombining. Both algorithms are shown to yield accurate construct-matching in a few minutes (even on hardware with limited processing power), together with a set of metrics that can be used to improve the robustness of the decision-making process. To ensure reliability and reproducibility, cMatch builds on the highly validated pairwise-matching Smith-Waterman algorithm. All the tests presented have been conducted on synthetic data for challenging, yet realistic constructs - and on real data gathered during studies on a metabolic engineering example (lycopene production).
Collapse
Affiliation(s)
- Alexis Casas
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Matthieu Bultelle
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Charles Motraghi
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Richard Kitney
- Department of Bioengineering, Imperial College London, London, United Kingdom
| |
Collapse
|
15
|
Xie Y, Chen S, Xiong X. Metabolic Engineering of Non-carotenoid-Producing Yeast Yarrowia lipolytica for the Biosynthesis of Zeaxanthin. Front Microbiol 2021; 12:699235. [PMID: 34690947 PMCID: PMC8529107 DOI: 10.3389/fmicb.2021.699235] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/30/2021] [Indexed: 01/29/2023] Open
Abstract
Zeaxanthin is vital to human health; thus, its production has received much attention, and it is also an essential precursor for the biosynthesis of other critical carotenoids such as astaxanthin and crocetin. Yarrowia lipolytica is one of the most intensively studied non-conventional yeasts and has been genetically engineered as a cell factory to produce carotenoids such as lycopene and β-carotene. However, zeaxanthin production by Y. lipolytica has not been well investigated. To fill this gap, β-carotene biosynthesis pathway has been first constructed in this study by the expression of genes, including crtE, crtB, crtI, and carRP. Three crtZ genes encoding β-carotene hydroxylase from different organisms were individually introduced into β-carotene-producing Y. lipolytica to evaluate their performance for producing zeaxanthin. The expression of crtZ from the bacterium Pantoea ananatis (formerly Erwinia uredovora, Eu-crtZ) resulted in the highest zeaxanthin titer and content on the basis of dry cell weight (DCW). After verifying the function of Eu-crtZ for producing zeaxanthin, the high-copy-number integration into the ribosomal DNA of Y. lipolytica led to a 4.02-fold increase in the titer of zeaxanthin and a 721% increase in the content of zeaxanthin. The highest zeaxanthin titer achieved 21.98 ± 1.80 mg/L by the strain grown on a yeast extract peptone dextrose (YPD)–rich medium. In contrast, the highest content of DCW reached 3.20 ± 0.11 mg/g using a synthetic yeast nitrogen base (YNB) medium to culture the cells. Over 18.0 g/L of citric acid was detected in the supernatant of the YPD medium at the end of cultivation. Furthermore, the zeaxanthin-producing strains still accumulated a large amount of lycopene and β-carotene. The results demonstrated the potential of a cell factory for zeaxanthin biosynthesis and opened up an avenue to engineer this host for the overproduction of carotenoids.
Collapse
Affiliation(s)
- Yuxiao Xie
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Shulin Chen
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| | - Xiaochao Xiong
- Department of Biological Systems Engineering, Washington State University, Pullman, WA, United States
| |
Collapse
|
16
|
Zafar J, Aqeel A, Shah FI, Ehsan N, Gohar UF, Moga MA, Festila D, Ciurea C, Irimie M, Chicea R. Biochemical and Immunological implications of Lutein and Zeaxanthin. Int J Mol Sci 2021; 22:10910. [PMID: 34681572 PMCID: PMC8535525 DOI: 10.3390/ijms222010910] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 09/27/2021] [Accepted: 10/03/2021] [Indexed: 12/21/2022] Open
Abstract
Throughout history, nature has been acknowledged for being a primordial source of various bioactive molecules in which human macular carotenoids are gaining significant attention. Among 750 natural carotenoids, lutein, zeaxanthin and their oxidative metabolites are selectively accumulated in the macular region of living beings. Due to their vast applications in food, feed, pharmaceutical and nutraceuticals industries, the global market of lutein and zeaxanthin is continuously expanding but chemical synthesis, extraction and purification of these compounds from their natural repertoire e.g., plants, is somewhat costly and technically challenging. In this regard microbial as well as microalgal carotenoids are considered as an attractive alternative to aforementioned challenges. Through the techniques of genetic engineering and gene-editing tools like CRISPR/Cas9, the overproduction of lutein and zeaxanthin in microorganisms can be achieved but the commercial scale applications of such procedures needs to be done. Moreover, these carotenoids are highly unstable and susceptible to thermal and oxidative degradation. Therefore, esterification of these xanthophylls and microencapsulation with appropriate wall materials can increase their shelf-life and enhance their application in food industry. With their potent antioxidant activities, these carotenoids are emerging as molecules of vital importance in chronic degenerative, malignancies and antiviral diseases. Therefore, more research needs to be done to further expand the applications of lutein and zeaxanthin.
Collapse
Affiliation(s)
- Javaria Zafar
- Institute of Industrial Biotechnology, Government College University Lahore, Lahore 54000, Pakistan; (J.Z.); (A.A.); (F.I.S.); (N.E.); (U.F.G.)
| | - Amna Aqeel
- Institute of Industrial Biotechnology, Government College University Lahore, Lahore 54000, Pakistan; (J.Z.); (A.A.); (F.I.S.); (N.E.); (U.F.G.)
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University Lahore, Lahore 54000, Pakistan; (J.Z.); (A.A.); (F.I.S.); (N.E.); (U.F.G.)
| | - Naureen Ehsan
- Institute of Industrial Biotechnology, Government College University Lahore, Lahore 54000, Pakistan; (J.Z.); (A.A.); (F.I.S.); (N.E.); (U.F.G.)
| | - Umar Farooq Gohar
- Institute of Industrial Biotechnology, Government College University Lahore, Lahore 54000, Pakistan; (J.Z.); (A.A.); (F.I.S.); (N.E.); (U.F.G.)
| | - Marius Alexandru Moga
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (M.A.M.); (M.I.)
| | - Dana Festila
- Radiology and Maxilo Facial Surgery Department, Iuliu Hatieganu University of Medicine and Pharmacy, 400012 Cluj Napoca, Romania
| | - Codrut Ciurea
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (M.A.M.); (M.I.)
| | - Marius Irimie
- Faculty of Medicine, Transilvania University of Brasov, 500036 Brasov, Romania; (M.A.M.); (M.I.)
| | - Radu Chicea
- Faculty of Medicine, “Lucian Blaga” University, 550169 Sibiu, Romania;
| |
Collapse
|
17
|
Clostridium thermocellum as a Promising Source of Genetic Material for Designer Cellulosomes: An Overview. Catalysts 2021. [DOI: 10.3390/catal11080996] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Plant biomass-based biofuels have gradually substituted for conventional energy sources thanks to their obvious advantages, such as renewability, huge quantity, wide availability, economic feasibility, and sustainability. However, to make use of the large amount of carbon sources stored in the plant cell wall, robust cellulolytic microorganisms are highly demanded to efficiently disintegrate the recalcitrant intertwined cellulose fibers to release fermentable sugars for microbial conversion. The Gram-positive, thermophilic, cellulolytic bacterium Clostridium thermocellum possesses a cellulolytic multienzyme complex termed the cellulosome, which has been widely considered to be nature’s finest cellulolytic machinery, fascinating scientists as an auspicious source of saccharolytic enzymes for biomass-based biofuel production. Owing to the supra-modular characteristics of the C. thermocellum cellulosome architecture, the cellulosomal components, including cohesin, dockerin, scaffoldin protein, and the plentiful cellulolytic and hemicellulolytic enzymes have been widely used for constructing artificial cellulosomes for basic studies and industrial applications. In addition, as the well-known microbial workhorses are naïve to biomass deconstruction, several research groups have sought to transform them from non-cellulolytic microbes into consolidated bioprocessing-enabling microbes. This review aims to update and discuss the current progress in these mentioned issues, point out their limitations, and suggest some future directions.
Collapse
|
18
|
Growth Enhancement Facilitated by Gaseous CO2 through Heterologous Expression of Reductive Tricarboxylic Acid Cycle Genes in Escherichia coli. FERMENTATION 2021. [DOI: 10.3390/fermentation7020098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The enzymatic mechanisms of carbon fixation by autotrophs, such as the reductive tricarboxylic acid cycle (rTCA), have inspired biotechnological approaches to producing bio-based chemicals directly through CO2. To explore the possibility of constructing an rTCA cycle in Escherichia coli and to investigate their potential for CO2 assimilation, a total of ten genes encoding the key rTCA cycle enzymes, including α-ketoglutarate:ferredoxin oxidoreductase, ATP-dependent citrate lyase, and fumarate reductase/succinate dehydrogenase, were cloned into E. coli. The transgenic E. coli strain exhibited enhanced growth and the ability to assimilate external inorganic carbon with a gaseous CO2 supply. Further experiments conducted in sugar-free medium containing hydrogen as the electron donor and dimethyl sulfoxide (DMSO) as the electron acceptor proved that the strain is able to undergo anaerobic respiration, using CO2 as the major carbon source. The transgenic stain demonstrated CO2-enhanced growth, whereas the genes involved in chemotaxis, flagellar assembly, and acid-resistance were upregulated under the anaerobic respiration. Furthermore, metabolomic analysis demonstrated that the total concentrations of ATP, ADP, and AMP in the transgenic strain were higher than those in the vector control strain and these results coincided with the enhanced growth. Our approach offers a novel strategy to engineer E. coli for assimilating external gaseous CO2.
Collapse
|
19
|
One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE). mSystems 2021; 6:e0018121. [PMID: 34042466 PMCID: PMC8269212 DOI: 10.1128/msystems.00181-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Soil harbors arguably the most metabolically and genetically heterogeneous microbiomes on Earth, yet establishing the link between metabolic functions and genome at the precisely one-cell level has been difficult. Here, for mock microbial communities and then for soil microbiota, we established a Raman-activated gravity-driven single-cell encapsulation and sequencing (RAGE-Seq) platform, which identifies, sorts, and sequences precisely one bacterial cell via its anabolic (incorporating D from heavy water) and physiological (carotenoid-containing) functions. We showed that (i) metabolically active cells from numerically rare soil taxa, such as Corynebacterium spp., Clostridium spp., Moraxella spp., Pantoea spp., and Pseudomonas spp., can be readily identified and sorted based on D2O uptake, and their one-cell genome coverage can reach ∼93% to allow high-quality genome-wide metabolic reconstruction; (ii) similarly, carotenoid-containing cells such as Pantoea spp., Legionella spp., Massilia spp., Pseudomonas spp., and Pedobacter spp. were identified and one-cell genomes were generated for tracing the carotenoid-synthetic pathways; and (iii) carotenoid-producing cells can be either metabolically active or inert, suggesting culture-based approaches can miss many such cells. As a Raman-activated cell sorter (RACS) family member that can establish a metabolism-genome link at exactly one-cell resolution from soil, RAGE-Seq can help to precisely pinpoint “who is doing what” in complex ecosystems. IMPORTANCE Soil is home to an enormous and complex microbiome that features arguably the highest genomic diversity and metabolic heterogeneity of cells on Earth. Their in situ metabolic activities drive many natural processes of pivotal ecological significance or underlie industrial production of numerous valuable bioactivities. However, pinpointing “who is doing what” in a soil microbiome, which consists of mainly yet-to-be-cultured species, has remained a major challenge. Here, for soil microbiota, we established a Raman-activated gravity-driven single-cell encapsulation and sequencing (RAGE-Seq) method, which identifies, sorts, and sequences at the resolution of precisely one microbial cell via its catabolic and anabolic functions. As a Raman-activated cell sorter (RACS) family member that can establish a metabolism-genome link at one-cell resolution from soil, RAGE-Seq can help to precisely pinpoint “who is doing what” in complex ecosystems.
Collapse
|
20
|
Liu T, Luo H, Gao F. Position preference of essential genes in prokaryotic operons. PLoS One 2021; 16:e0250380. [PMID: 33886641 PMCID: PMC8061932 DOI: 10.1371/journal.pone.0250380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/05/2021] [Indexed: 11/19/2022] Open
Abstract
Essential genes, which form the basis of life activities, are crucial for the survival of organisms. Essential genes tend to be located in operons, but how they are distributed in operons is still unclear for most prokaryotes. In order to clarify the general rule of position preference of essential genes in operons, an index of the average position of genes in an operon was proposed, and the distributions of essential and non-essential genes in operons in 51 bacterial genomes and two archaeal genomes were analyzed based on this new index. Consequently, essential genes were found to preferentially occupy the front positions of the operons, which tend to be expressed at higher levels.
Collapse
Affiliation(s)
- Tao Liu
- Department of Physics, School of Science, Tianjin University, Tianjin, China
| | - Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin, China
- * E-mail: (FG); (HL)
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
- * E-mail: (FG); (HL)
| |
Collapse
|
21
|
Gilman J, Walls L, Bandiera L, Menolascina F. Statistical Design of Experiments for Synthetic Biology. ACS Synth Biol 2021; 10:1-18. [PMID: 33406821 DOI: 10.1021/acssynbio.0c00385] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The design and optimization of biological systems is an inherently complex undertaking that requires careful balancing of myriad synergistic and antagonistic variables. However, despite this complexity, much synthetic biology research is predicated on One Factor at A Time (OFAT) experimentation; the genetic and environmental variables affecting the activity of a system of interest are sequentially altered while all other variables are held constant. Beyond being time and resource intensive, OFAT experimentation crucially ignores the effect of interactions between factors. Given the ubiquity of interacting genetic and environmental factors in biology this failure to account for interaction effects in OFAT experimentation can result in the development of suboptimal systems. To address these limitations, an increasing number of studies have turned to Design of Experiments (DoE), a suite of methods that enable efficient, systematic exploration and exploitation of complex design spaces. This review provides an overview of DoE for synthetic biologists. Key concepts and commonly used experimental designs are introduced, and we discuss the advantages of DoE as compared to OFAT experimentation. We dissect the applicability of DoE in the context of synthetic biology and review studies which have successfully employed these methods, illustrating the potential of statistical experimental design to guide the design, characterization, and optimization of biological protocols, pathways, and processes.
Collapse
Affiliation(s)
- James Gilman
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Laura Walls
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Lucia Bandiera
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9YL, U.K
| | - Filippo Menolascina
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH8 9YL, U.K
| |
Collapse
|
22
|
Godara A, Kao KC. Adaptive laboratory evolution for growth coupled microbial production. World J Microbiol Biotechnol 2020; 36:175. [DOI: 10.1007/s11274-020-02946-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/08/2020] [Indexed: 12/18/2022]
|
23
|
Chromosome Engineering To Generate Plasmid-Free Phenylalanine- and Tyrosine-Overproducing Escherichia coli Strains That Can Be Applied in the Generation of Aromatic-Compound-Producing Bacteria. Appl Environ Microbiol 2020; 86:AEM.00525-20. [PMID: 32414798 DOI: 10.1128/aem.00525-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/11/2020] [Indexed: 12/25/2022] Open
Abstract
Many phenylalanine- and tyrosine-producing strains have used plasmid-based overexpression of pathway genes. The resulting strains achieved high titers and yields of phenylalanine and tyrosine. Chromosomally engineered, plasmid-free producers have shown lower titers and yields than plasmid-based strains, but the former are advantageous in terms of cultivation cost and public health/environmental risk. Therefore, we engineered here the Escherichia coli chromosome to create superior phenylalanine- and tyrosine-overproducing strains that did not depend on plasmid-based expression. Integration into the E. coli chromosome of two central metabolic pathway genes (ppsA and tktA) and eight shikimate pathway genes (aroA, aroB, aroC, aroD, aroE, aroGfbr , aroL, and pheAfbr ), controlled by the T7lac promoter, resulted in excellent titers and yields of phenylalanine; the superscript "fbr" indicates that the enzyme encoded by the gene was feedback resistant. The generated strain could be changed to be a superior tyrosine-producing strain by replacing pheAfbr with tyrAfbr A rational approach revealed that integration of seven genes (ppsA, tktA, aroA, aroB, aroC, aroGfbr , and pheAfbr ) was necessary as the minimum gene set for high-yield phenylalanine production in E. coli MG1655 (tyrR, adhE, ldhA, pykF, pflDC, and ascF deletant). The phenylalanine- and tyrosine-producing strains were further applied to generate phenyllactic acid-, 4-hydroxyphenyllactic acid-, tyramine-, and tyrosol-producing strains; yield of these aromatic compounds increased proportionally to the increase in phenylalanine and tyrosine yields.IMPORTANCE Plasmid-free strains for aromatic compound production are desired in the aspect of industrial application. However, the yields of phenylalanine and tyrosine have been considerably lower in plasmid-free strains than in plasmid-based strains. The significance of this research is that we succeeded in generating superior plasmid-free phenylalanine- and tyrosine-producing strains by engineering the E. coli chromosome, which was comparable to that in plasmid-based strains. The generated strains have a potential to generate superior strains for the production of aromatic compounds. Actually, we demonstrated that four kinds of aromatic compounds could be produced from glucose with high yields (e.g., 0.28 g tyrosol/g glucose).
Collapse
|
24
|
Zheng Y, Meng F, Zhu Z, Wei W, Sun Z, Chen J, Yu B, Lou C, Chen GQ. A tight cold-inducible switch built by coupling thermosensitive transcriptional and proteolytic regulatory parts. Nucleic Acids Res 2020; 47:e137. [PMID: 31750522 PMCID: PMC6868347 DOI: 10.1093/nar/gkz785] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/30/2019] [Accepted: 09/04/2019] [Indexed: 12/20/2022] Open
Abstract
Natural organisms have evolved intricate regulatory mechanisms that sense and respond to fluctuating environmental temperatures in a heat- or cold-inducible fashion. Unlike dominant heat-inducible switches, very few cold-inducible genetic switches are available in either natural or engineered systems. Moreover, the available cold-inducible switches still have many shortcomings, including high leaky gene expression, small dynamic range (<10-fold) or broad transition temperature (>10°C). To address these problems, a high-performance cold-inducible switch that can tightly control target gene expression is highly desired. Here, we introduce a tight and fast cold-inducible switch that couples two evolved thermosensitive variants, TFts and TEVts, as well as an additional Mycoplasma florum Lon protease (mf-Lon) to effectively turn-off target gene expression via transcriptional and proteolytic mechanisms. We validated the function of the switch in different culture media and various Escherichia coli strains and demonstrated its tightness by regulating two morphogenetic bacterial genes and expressing three heat-unstable recombinant proteins, respectively. Moreover, the additional protease module enabled the cold-inducible switch to actively remove the pre-existing proteins in slow-growing cells. This work establishes a high-performance cold-inducible system for tight and fast control of gene expression which has great potential for basic research, as well as industrial and biomedical applications.
Collapse
Affiliation(s)
- Yang Zheng
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fankang Meng
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Zihui Zhu
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weijia Wei
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Zhi Sun
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China
| | - Jinchun Chen
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunbo Lou
- CAS Key Laboratory of Microbial Physiological & Metabolic Engineering and State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100149, China.,College of Life Science, University of Science and Technology of China, Hefei 230027, China
| | - Guo-Qiang Chen
- MOE Key Lab of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,MOE Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| |
Collapse
|
25
|
Liu M, Sandmann G, Chen F, Huang J. Enhanced Coproduction of Cell-Bound Zeaxanthin and Secreted Exopolysaccharides by Sphingobium sp. via Metabolic Engineering and Optimized Fermentation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12228-12236. [PMID: 31638826 DOI: 10.1021/acs.jafc.9b05342] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Zeaxanthin is a value-added carotenoid with wide applications. This study aims to manipulate a generally recognized as safe and carotenoid-producing bacterium, Sphingobium sp., for enhanced production of zeaxanthin and exopolysaccharides. First, whole-genome sequencing and analysis of pathway genes were applied to define the carotenoid pathway in Sphingobium sp. Second, a Sphingobium transformation system was established to engineer metabolite flux into zeaxanthin. By a combination of chemical mutagenesis and removal of bottlenecks of carotenoid biosynthesis via overexpression of three rate-limiting enzymes, the genetically modified Sphingobium DIZ strain produced 21.26 mg/g dry cell weight of zeaxanthin, which was about 4-fold higher than the wild type. Upon optimization of culture conditions, the DIZ strain produced 479.5 mg/L of zeaxanthin with the productivity of 4.99 mg/L/h and 21.9 g/L of exopolysaccharides using a fed-batch fermentation strategy. This study represents the first genetic manipulation of Sphingobium sp., a biotechnologically important bacterium, for high-yield production of value-added metabolites.
Collapse
Affiliation(s)
- Mengmeng Liu
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany , Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049 , People's Republic of China
| | - Gerhard Sandmann
- Institute of Molecular Bioscience , J.W. Goethe Universitat , Max von Laue Str. 9 , Frankfurt 60438 , Germany
| | - Feng Chen
- Institute for Advanced Study , Shenzhen University , Shenzhen 518060 , People's Republic of China
| | - Junchao Huang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany , Chinese Academy of Sciences , Kunming 650201 , People's Republic of China
| |
Collapse
|
26
|
Becker J, Wittmann C. A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products. Biotechnol Adv 2019; 37:107360. [DOI: 10.1016/j.biotechadv.2019.02.016] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
|
27
|
Godara A, Rodriguez MAG, Weatherston JD, Peabody GL, Wu HJ, Kao KC. Beneficial mutations for carotenoid production identified from laboratory-evolved Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2019; 46:1793-1804. [PMID: 31595456 DOI: 10.1007/s10295-019-02241-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/26/2019] [Indexed: 01/26/2023]
Abstract
Adaptive laboratory evolution (ALE) is a powerful tool used to increase strain fitness in the presence of environmental stressors. If production and strain fitness can be coupled, ALE can be used to increase product formation. In earlier work, carotenoids hyperproducing mutants were obtained using an ALE strategy. Here, de novo mutations were identified in hyperproducers, and reconstructed mutants were explored to determine the exact impact of each mutation on production and tolerance. A single mutation in YMRCTy1-3 conferred increased carotenoid production, and when combined with other beneficial mutations led to further increased β-carotene production. Findings also suggest that the ALE strategy selected for mutations that confer increased carotenoid production as primary phenotype. Raman spectroscopy analysis and total lipid quantification revealed positive correlation between increased lipid content and increased β-carotene production. Finally, we demonstrated that the best combinations of mutations identified for β-carotene production were also beneficial for production of lycopene.
Collapse
Affiliation(s)
- Avinash Godara
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Joshua D Weatherston
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | | | - Hung-Jen Wu
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Katy C Kao
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA. .,Department of Chemical and Materials Engineering, San Jose State University, One Washington Square, San Jose, CA, 95129, USA.
| |
Collapse
|
28
|
Wu Z, Zhao D, Li S, Wang J, Bi C, Zhang X. Combinatorial modulation of initial codons for improved zeaxanthin synthetic pathway efficiency in Escherichia coli. Microbiologyopen 2019; 8:e930. [PMID: 31532062 PMCID: PMC6925171 DOI: 10.1002/mbo3.930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 11/09/2022] Open
Abstract
A balanced and optimized metabolic pathway is the basis for efficient production of a target metabolite. Traditional strategies mostly involve the manipulation of promoters or ribosome-binding sites, which can encompass long sequences and can be complex to operate. In this work, we found that by changing only the three nucleotides of the initiation codons, expression libraries of reporter proteins RFP, GFP, and lacZ with a large dynamic range and evenly distributed expression levels could be established in Escherichia coli (E. coli). Thus, a novel strategy that uses combinatorial modulation of initial codons (CMIC) was developed for metabolic pathway optimization and applied to the three genes crtZ, crtY, and crtI of the zeaxanthin synthesis pathway in E. coli. The initial codons of these genes were changed to random nucleotides NNN, and the gene cassettes were assembled into vectors via an optimized strategy based on type II restriction enzymes. With minimal labor time, a combinatorial library was obtained containing strains with various zeaxanthin production levels, including a strain with a titer of 6.33 mg/L and specific production value of 1.24 mg/g DCW-a striking 10-fold improvement over the starting strain. The results demonstrated that CMIC was a feasible technique for conveniently optimizing metabolic pathways. To our best knowledge, this is the first metabolic engineering strategy that relies on manipulating the initiation codons for pathway optimization in E. coli.
Collapse
Affiliation(s)
- Zaiqiang Wu
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Junsong Wang
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Park, Tianjin, 300308, China
| |
Collapse
|
29
|
Marine Biosurfactants: Biosynthesis, Structural Diversity and Biotechnological Applications. Mar Drugs 2019; 17:md17070408. [PMID: 31323998 PMCID: PMC6669457 DOI: 10.3390/md17070408] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 07/04/2019] [Accepted: 07/07/2019] [Indexed: 11/16/2022] Open
Abstract
Biosurfactants are amphiphilic secondary metabolites produced by microorganisms. Marine bacteria have recently emerged as a rich source for these natural products which exhibit surface-active properties, making them useful for diverse applications such as detergents, wetting and foaming agents, solubilisers, emulsifiers and dispersants. Although precise structural data are often lacking, the already available information deduced from biochemical analyses and genome sequences of marine microbes indicates a high structural diversity including a broad spectrum of fatty acid derivatives, lipoamino acids, lipopeptides and glycolipids. This review aims to summarise biosyntheses and structures with an emphasis on low molecular weight biosurfactants produced by marine microorganisms and describes various biotechnological applications with special emphasis on their role in the bioremediation of oil-contaminated environments. Furthermore, novel exploitation strategies are suggested in an attempt to extend the existing biosurfactant portfolio.
Collapse
|
30
|
Taniguchi H, Imura M, Okano K, Honda K. Developing a single strain for in vitro salvage synthesis of NAD + at high temperatures and its potential for bioconversion. Microb Cell Fact 2019; 18:75. [PMID: 31023312 PMCID: PMC6482498 DOI: 10.1186/s12934-019-1125-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/22/2019] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Thermostable enzymes have several advantages over their mesophilic counterparts for industrial applications. However, trade-offs such as thermal instability of enzyme substrates or co-factors exist. Nicotinamide adenine dinucleotide (NAD+) is an important co-factor in many enzyme-catalyzed oxidation-reduction reactions. This compound spontaneously decomposes at elevated temperatures and basic pH, a property that limits catalysis of NAD+/NADH-dependent bioconversions using thermostable enzymes to short timeframes. To address this issue, an "in vitro metabolic pathway" for salvage synthesis of NAD+ using six thermophilic enzymes was constructed to resynthesize NAD+ from its thermal decomposition products at high temperatures. RESULTS An integrated strain, E. coli DH5α (pBR-CI857, pGETS118-NAD+), that codes for six thermophilic enzymes in a single operon was constructed. Gene-expression levels of these enzymes in the strain were modulated by their sequential order in the operon. An enzyme solution containing these enzymes was prepared by the heat purification from the cell lysate of the integrated strain, and used as an enzyme cocktail for salvage synthesis of NAD+. The salvage activity for synthesis of NAD+ from its thermal decomposition products was found to be 0.137 ± 0.006 µmol min-1 g-1 wet cells. More than 50% of this initial activity remained after 24 h at 60 °C. The enzyme cocktail could maintain a NAD+ concentration of 1 mM for 12 h at 60 °C. Furthermore, this enzyme cocktail supported continuous NAD+/NADH-dependent redox reactions using only NAD+/NADH derived from host cells, without the need for addition of external NAD+. CONCLUSIONS The integrated strain allows preparation of an enzyme cocktail that can solve the problem of NAD+ instability at high temperatures. The strain simplifies preparation of the enzyme cocktail, and thus expands the applicability of the in vitro metabolic engineering method using thermostable enzymes. Further optimization of gene expressions in the integrated strain can be achieved by using various types of ribosome binding sites as well as promoters.
Collapse
Affiliation(s)
- Hironori Taniguchi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
| | - Makoto Imura
- KOHJIN Life Sciences Co., Ltd., Higashihama 1-6, Saiki, Oita, 876-858, Japan
| | - Kenji Okano
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan
| | - Kohsuke Honda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Yamadaoka 2-1, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
31
|
Ghosh IN, Martien J, Hebert AS, Zhang Y, Coon JJ, Amador-Noguez D, Landick R. OptSSeq explores enzyme expression and function landscapes to maximize isobutanol production rate. Metab Eng 2019; 52:324-340. [DOI: 10.1016/j.ymben.2018.12.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/26/2018] [Accepted: 12/25/2018] [Indexed: 10/27/2022]
|
32
|
Akay A, Hess H. Deep Learning: Current and Emerging Applications in Medicine and Technology. IEEE J Biomed Health Inform 2019; 23:906-920. [PMID: 30676989 DOI: 10.1109/jbhi.2019.2894713] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Machine learning is enabling researchers to analyze and understand increasingly complex physical and biological phenomena in traditional fields such as biology, medicine, and engineering and emerging fields like synthetic biology, automated chemical synthesis, and biomanufacturing. These fields require new paradigms toward understanding increasingly complex data and converting such data into medical products and services for patients. The move toward deep learning and complex modeling is an attempt to bridge the gap between acquiring massive quantities of complex data, and converting such data into practical insights. Here, we provide an overview of the field of machine learning, its current applications and needs in traditional and emerging fields, and discuss an illustrative attempt at using deep learning to understand swarm behavior of molecular shuttles.
Collapse
|
33
|
Okano K, Honda K, Taniguchi H, Kondo A. De novo design of biosynthetic pathways for bacterial production of bulk chemicals and biofuels. FEMS Microbiol Lett 2018; 365:5087733. [DOI: 10.1093/femsle/fny215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 08/29/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Kenji Okano
- Synthetic Bioengineering Laboratory, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565–0871, Japan
| | - Kohsuke Honda
- Synthetic Bioengineering Laboratory, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565–0871, Japan
| | - Hironori Taniguchi
- Synthetic Bioengineering Laboratory, Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565–0871, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657–8501, Japan
| |
Collapse
|
34
|
Zou H, Zhang T, Li L, Huang J, Zhang N, Shi M, Hao H, Xian M. Systematic Engineering for Improved Carbon Economy in the Biosynthesis of Polyhydroxyalkanoates and Isoprenoids. MATERIALS (BASEL, SWITZERLAND) 2018; 11:E1271. [PMID: 30042344 PMCID: PMC6117667 DOI: 10.3390/ma11081271] [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: 06/06/2018] [Revised: 07/10/2018] [Accepted: 07/19/2018] [Indexed: 11/23/2022]
Abstract
With the rapid development of synthetic biology and metabolic engineering, a broad range of biochemicals can be biosynthesized, which include polyhydroxyalkanoates and isoprenoids. However, some of the bio-approaches in chemical synthesis have just started to be applied outside of laboratory settings, and many require considerable efforts to achieve economies of scale. One of the often-seen barriers is the low yield and productivity, which leads to higher unit cost and unit capital investment for the bioconversion process. In general, higher carbon economy (less carbon wastes during conversion process from biomass to objective bio-based chemicals) will result in higher bioconversion yield, which results in less waste being generated during the process. To achieve this goal, diversified strategies have been applied; matured strategies include pathway engineering to block competitive pathways, enzyme engineering to enhance the activities of enzymes, and process optimization to improve biomass/carbon yield. In this review, we analyze the impact of carbon sources from different types of biomass on the yield of bio-based chemicals (especially for polyhydroxyalkanoates and isoprenoids). Moreover, we summarize the traditional strategies for improving carbon economy during the bioconversion process and introduce the updated techniques in building up non-natural carbon pathways, which demonstrate higher carbon economies than their natural counterparts.
Collapse
Affiliation(s)
- Huibin Zou
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| | - Tongtong Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Lei Li
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Jingling Huang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Nan Zhang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Mengxun Shi
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - He Hao
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
| | - Mo Xian
- CAS Key Laboratory of Bio-based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.
| |
Collapse
|
35
|
Oyetunde T, Bao FS, Chen JW, Martin HG, Tang YJ. Leveraging knowledge engineering and machine learning for microbial bio-manufacturing. Biotechnol Adv 2018; 36:1308-1315. [DOI: 10.1016/j.biotechadv.2018.04.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/27/2018] [Accepted: 04/26/2018] [Indexed: 12/21/2022]
|
36
|
Chang JJ, Anandharaj M, Ho CY, Tsuge K, Tsai TY, Ke HM, Lin YJ, Ha Tran MD, Li WH, Huang CC. Biomimetic strategy for constructing Clostridium thermocellum cellulosomal operons in Bacillus subtilis. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:157. [PMID: 29930703 PMCID: PMC5991470 DOI: 10.1186/s13068-018-1151-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/23/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Enzymatic conversion of lignocellulosic biomass into soluble sugars is a major bottleneck in the plant biomass utilization. Several anaerobic organisms cope these issues via multiple-enzyme complex system so called 'cellulosome'. Hence, we proposed a "biomimic operon" concept for making an artificial cellulosome which can be used as a promising tool for the expression of cellulosomal enzymes in Bacillus subtilis. RESULTS According to the proteomic analysis of Clostridium thermocellum ATCC27405 induced by Avicel or cellobiose, we selected eight highly expressed cellulosomal genes including a scaffoldin protein gene (cipA), a cell-surface anchor gene (sdbA), two exoglucanase genes (celK and celS), two endoglucanase genes (celA and celR), and two xylanase genes (xynC and xynZ). Arranging these eight genes in two different orders, we constructed two different polycistronic operons using the ordered gene assembly in Bacillus method. This is the first study to express the whole CipA along with cellulolytic enzymes in B. subtilis. Each operon was successfully expressed in B. subtilis RM125, and the protein complex assembly, cellulose-binding ability, thermostability, and cellulolytic activity were demonstrated. The operon with a higher xylanase activity showed greater saccharification on complex cellulosic substrates such as Napier grass than the other operon. CONCLUSIONS In this study, a strategy for constructing an efficient cellulosome system was developed and two different artificial cellulosomal operons were constructed. Both operons could efficiently express the cellulosomal enzymes and exhibited cellulose saccharification. This strategy can be applied to different industries with cellulose-containing materials, such as papermaking, biofuel, agricultural compost, mushroom cultivation, and waste processing industries.
Collapse
Affiliation(s)
- Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 402 Taiwan
| | - Marimuthu Anandharaj
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Cheng-Yu Ho
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Kenji Tsuge
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihoji, Tsuruoka, Yamagata 997-0017 Japan
| | - Tsung-Yu Tsai
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Huei-Mien Ke
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Yu-Ju Lin
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
| | - Minh Dung Ha Tran
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, 11529 Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, 11529 Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227 Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 40227 Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227 Taiwan
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, 40227 Taiwan
| |
Collapse
|
37
|
Huang W, Lin Y, He M, Gong Y, Huang J. Induced High-Yield Production of Zeaxanthin, Lutein, and β-Carotene by a Mutant of Chlorella zofingiensis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:891-897. [PMID: 29319312 DOI: 10.1021/acs.jafc.7b05400] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Natural resources of zeaxanthin are extremely limited. A Chlorella zofingiensis mutant (CZ-bkt1), which could accumulate high amounts of zeaxanthin, was generated and characterized. CZ-bkt1 was achieved by treating the algal cells with a chemical mutagen followed by a color-based colony-screening approach. CZ-bkt1 was found to consist of a dysfunctional carotenoid ketolase, leading to the accumulation of zeaxanthin rather than to its downstream ketocarotenoid astaxanthin. Light irradiation, glucose, NaCl, and nitrogen deficiency all induced CZ-bkt1 to accumulate zeaxanthin. CZ-bkt1 accumulated zeaxanthin up to 7.00 ± 0.82 mg/g when induced by high-light irradiation and nitrogen deficiency and up to 36.79 ± 2.23 mg/L by additional feeding with glucose. Furthermore, in addition to zeaxanthin, CZ-bkt1 also accumulated high amounts of β-carotene (7.18 ± 0.72 mg/g or 34.64 ± 1.39 mg/L) and lutein (13.81 ± 1.23 mg/g or 33.97 ± 2.61 mg/L). CZ-bkt1 is the sole species up to date with the ability to accumulate high amounts of the three carotenoids that are essential for human health.
Collapse
Affiliation(s)
- Weiping Huang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Yan Lin
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Mingxia He
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Yuhao Gong
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| | - Junchao Huang
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650201, China
| |
Collapse
|
38
|
Efficient production of lycopene by engineered E. coli strains harboring different types of plasmids. Bioprocess Biosyst Eng 2018; 41:489-499. [DOI: 10.1007/s00449-017-1883-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/14/2017] [Indexed: 02/02/2023]
|
39
|
Andreou AI, Nakayama N. Mobius Assembly: A versatile Golden-Gate framework towards universal DNA assembly. PLoS One 2018; 13:e0189892. [PMID: 29293531 PMCID: PMC5749717 DOI: 10.1371/journal.pone.0189892] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/04/2017] [Indexed: 11/26/2022] Open
Abstract
Synthetic biology builds upon the foundation of engineering principles, prompting innovation and improvement in biotechnology via a design-build-test-learn cycle. A community-wide standard in DNA assembly would enable bio-molecular engineering at the levels of predictivity and universality in design and construction that are comparable to other engineering fields. Golden Gate Assembly technology, with its robust capability to unidirectionally assemble numerous DNA fragments in a one-tube reaction, has the potential to deliver a universal standard framework for DNA assembly. While current Golden Gate Assembly frameworks (e.g. MoClo and Golden Braid) render either high cloning capacity or vector toolkit simplicity, the technology can be made more versatile-simple, streamlined, and cost/labor-efficient, without compromising capacity. Here we report the development of a new Golden Gate Assembly framework named Mobius Assembly, which combines vector toolkit simplicity with high cloning capacity. It is based on a two-level, hierarchical approach and utilizes a low-frequency cutter to reduce domestication requirements. Mobius Assembly embraces the standard overhang designs designated by MoClo, Golden Braid, and Phytobricks and is largely compatible with already available Golden Gate part libraries. In addition, dropout cassettes encoding chromogenic proteins were implemented for cost-free visible cloning screening that color-code different cloning levels. As proofs of concept, we have successfully assembled up to 16 transcriptional units of various pigmentation genes in both operon and multigene arrangements. Taken together, Mobius Assembly delivers enhanced versatility and efficiency in DNA assembly, facilitating improved standardization and automation.
Collapse
Affiliation(s)
- Andreas I. Andreou
- SynthSys Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Naomi Nakayama
- SynthSys Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Science at Extreme Condition, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
40
|
|
41
|
Zada B, Wang C, Park JB, Jeong SH, Park JE, Singh HB, Kim SW. Metabolic engineering of Escherichia coli for production of mixed isoprenoid alcohols and their derivatives. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:210. [PMID: 30061932 PMCID: PMC6058358 DOI: 10.1186/s13068-018-1210-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/19/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Current petroleum-derived fuels such as gasoline (C5-C12) and diesel (C15-C22) are complex mixtures of hydrocarbons with different chain lengths and chemical structures. Isoprenoids are hydrocarbon-based compounds with different carbon chain lengths and diverse chemical structures, similar to petroleum. Thus, isoprenoid alcohols such as isopentenol (C5), geraniol (C10), and farnesol (C15) have been considered to be ideal biofuel candidates. NudB, a native phosphatase of Escherichia coli, is reported to dephosphorylate isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) into isopentenol. However, no attention has been paid to its promiscuous activity toward longer chain length (C10-C15) prenyl diphosphates. RESULTS In this study, the promiscuous activity of NudB toward geranyl diphosphate (GPP) and farnesyl diphosphate (FPP) was applied for the production of isoprenoid alcohol mixtures, including isopentenol, geraniol, and farnesol, and their derivatives. E. coli was engineered to produce a mixture of C5 and C15 alcohols by overexpressing NudB (dihydroneopterin triphosphate diphosphohydrolase) and IspA (FPP synthase) along with a heterologous MVA pathway, which resulted in a total of up to 1652 mg/L mixture of C5 and C15 alcohols and their derivatives. The production was further increased to 2027 mg/L by overexpression of another endogenous phosphatase, AphA, in addition to NudB. Production of DMAPP- and FPP-derived alcohols and their derivatives was significantly increased with an increase in the gene dosage of idi, encoding IPP isomerase (IDI), indicating a potential modulation of the composition of the alcohols mixture according to the expression level of IDI. When IspA was replaced with its mutant IspA*, generating GPP in the production strain, a total of 1418 mg/L of the isoprenoid mixture was obtained containing C10 alcohols as a main component. CONCLUSIONS The promiscuous activity of NudB was newly identified and successfully used for production of isoprenoid-based alcohol mixtures, which are suitable as next-generation biofuels or commodity chemicals. This is the first successful report on high-titer production of an isoprenoid alcohol-based mixture. The engineering approaches can provide a valuable platform for production of other isoprenoid mixtures via a proportional modulation of IPP, DMAPP, GPP, and FPP syntheses.
Collapse
Affiliation(s)
- Bakht Zada
- Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Chonglong Wang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, People’s Republic of China
| | - Ji-Bin Park
- Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Seong-Hee Jeong
- Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Ju-Eon Park
- Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Hawaibam Birla Singh
- Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, 52828 Republic of Korea
| | - Seon-Won Kim
- Division of Applied Life Science (BK21 Plus Program), PMBBRC, Gyeongsang National University, Jinju, 52828 Republic of Korea
| |
Collapse
|
42
|
Niu FX, Lu Q, Bu YF, Liu JZ. Metabolic engineering for the microbial production of isoprenoids: Carotenoids and isoprenoid-based biofuels. Synth Syst Biotechnol 2017; 2:167-175. [PMID: 29318197 PMCID: PMC5655344 DOI: 10.1016/j.synbio.2017.08.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 08/03/2017] [Accepted: 08/09/2017] [Indexed: 12/22/2022] Open
Abstract
Isoprenoids are the most abundant and highly diverse group of natural products. Many isoprenoids have been used for pharmaceuticals, nutraceuticals, flavors, cosmetics, food additives and biofuels. Carotenoids and isoprenoid-based biofuels are two classes of important isoprenoids. These isoprenoids have been produced microbially through metabolic engineering and synthetic biology efforts. Herein, we briefly review the engineered biosynthetic pathways in well-characterized microbial systems for the production of carotenoids and several isoprenoid-based biofuels.
Collapse
Affiliation(s)
- Fu-Xing Niu
- Biotechnology Research Center and Biomedical Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Qian Lu
- Biotechnology Research Center and Biomedical Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yi-Fan Bu
- Biotechnology Research Center and Biomedical Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jian-Zhong Liu
- Biotechnology Research Center and Biomedical Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| |
Collapse
|
43
|
Chin WC, Lin KH, Liu CC, Tsuge K, Huang CC. Improved n-butanol production via co-expression of membrane-targeted tilapia metallothionein and the clostridial metabolic pathway in Escherichia coli. BMC Biotechnol 2017; 17:36. [PMID: 28399854 PMCID: PMC5387206 DOI: 10.1186/s12896-017-0356-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/22/2017] [Indexed: 11/10/2022] Open
Abstract
Background N-Butanol has favorable characteristics for use as either an alternative fuel or platform chemical. Bio-based n-butanol production using microbes is an emerging technology that requires further development. Although bio-industrial microbes such as Escherichia coli have been engineered to produce n-butanol, reactive oxygen species (ROS)-mediated toxicity may limit productivity. Previously, we show that outer-membrane-targeted tilapia metallothionein (OmpC-TMT) is more effective as an ROS scavenger than human and mouse metallothioneins to reduce oxidative stress in the host cell. Results The host strain (BUT1-DE) containing the clostridial n-butanol pathway displayed a decreased growth rate and limited n-butanol productivity, likely due to ROS accumulation. The clostridial n-butanol pathway was co-engineered with inducible OmpC-TMT in E. coli (BUT3-DE) for simultaneous ROS removal, and its effect on n-butanol productivity was examined. The ROS scavenging ability of cells overexpressing OmpC-TMT was examined and showed an approximately twofold increase in capacity. The modified strain improved n-butanol productivity to 320 mg/L, whereas the control strain produced only 95.1 mg/L. Transcriptomic analysis revealed three major KEGG pathways that were significantly differentially expressed in the BUT3-DE strain compared with their expression in the BUT1-DE strain, including genes involved in oxidative phosphorylation, fructose and mannose metabolism and glycolysis/gluconeogenesis. Conclusions These results indicate that OmpC-TMT can increase n-butanol production by scavenging ROS. The transcriptomic analysis suggested that n-butanol causes quinone malfunction, resulting in oxidative-phosphorylation-related nuo operon downregulation, which would diminish the ability to convert NADH to NAD+ and generate proton motive force. However, fructose and mannose metabolism-related genes (fucA, srlE and srlA) were upregulated, and glycolysis/gluconeogenesis-related genes (pfkB, pgm) were downregulated, which further assisted in regulating NADH/NAD+ redox and preventing additional ATP depletion. These results indicated that more NADH and ATP were required in the n-butanol synthetic pathway. Our study demonstrates a potential approach to increase the robustness of microorganisms and the production of toxic chemicals through the ability to reduce oxidative stress. Electronic supplementary material The online version of this article (doi:10.1186/s12896-017-0356-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Wei-Chih Chin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Kuo-Hsing Lin
- Center of Cold Chain Logistics Certification, College of Management, National Kaohsiung First University of Science and Technology, Kaohsiung, Taiwan
| | - Chun-Chi Liu
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan
| | - Kenji Tsuge
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan.
| |
Collapse
|
44
|
Lin CC, Yap CJS, Kan SC, Hsueh NC, Yang LY, Shieh CJ, Huang CC, Liu YC. Deciphering characteristics of the designer cellulosome from Bacillus subtilis WB800N via enzymatic analysis. Biochem Eng J 2017. [DOI: 10.1016/j.bej.2016.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
|
45
|
Sun J, Alper H. Synthetic Biology: An Emerging Approach for Strain Engineering. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Jie Sun
- Department of Chemical Engineering; The University of Texas at Austin; 200 E Dean Keeton Street Stop C0400, Austin TX 78712 USA
| | - Hal Alper
- Department of Chemical Engineering; The University of Texas at Austin; 200 E Dean Keeton Street Stop C0400, Austin TX 78712 USA
| |
Collapse
|
46
|
Shen HJ, Cheng BY, Zhang YM, Tang L, Li Z, Bu YF, Li XR, Tian GQ, Liu JZ. Dynamic control of the mevalonate pathway expression for improved zeaxanthin production in Escherichia coli and comparative proteome analysis. Metab Eng 2016; 38:180-190. [DOI: 10.1016/j.ymben.2016.07.012] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 06/07/2016] [Accepted: 07/25/2016] [Indexed: 01/13/2023]
|
47
|
Li Y, Wang G. Strategies of isoprenoids production in engineered bacteria. J Appl Microbiol 2016; 121:932-40. [DOI: 10.1111/jam.13237] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 06/24/2016] [Accepted: 07/14/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Y. Li
- College of Pharmaceutical and Biological Engineering; Shenyang University of Chemical Technology; Shenyang China
| | - G. Wang
- Key Laboratory of Environmental and Applied Microbiology; Chinese Academy of Sciences; Chengdu China
- Environmental Microbiology Key Laboratory of Sichuan Province; Chengdu Institute of Biology; Chinese Academy of Sciences; Chengdu China
| |
Collapse
|
48
|
Sun H, Zhao D, Xiong B, Zhang C, Bi C. Engineering Corynebacterium glutamicum for violacein hyper production. Microb Cell Fact 2016; 15:148. [PMID: 27557730 PMCID: PMC4997675 DOI: 10.1186/s12934-016-0545-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 08/15/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Corynebacterium glutamicum was used as a metabolic engineering chassis for production of crude violacein (mixture of violacein and deoxyviolacein) due to Corynebacterium's GRAS status and advantages in tryptophan fermentation. The violacein is a commercially potential compound with various applications derived from L-tryptophan. RESULTS Corynebacterium glutamicum ATCC 21850 that could produce 162.98 mg L(-1) tryptophan was employed as a novel host for metabolic engineering chassis. Heterologous vio operon from Chromobacterium violaceum was over-expressed in ATCC 21850 strain with constitutive promoter to have obtained 532 mg L(-1) violacein. Considering toxicity of violacein, vio operon was expressed with inducible promoter and 629 mg L(-1) violacein was obtained in batch culture. Due to the economical coding nature of vio operon, the compressed RBS of vio genes were replaced with complete strong C. glutamicum ones. And extended expression units were assembled to form a synthetic operon. With this strategy, 1116 mg L(-1) violacein in batch culture was achieved. Fermentation process was then optimized by studying induction time, induction concentration, culture composition and fermentation temperature. as a result, a titer of 5436 mg L(-1) and a productivity of 47 mg L(-1) h(-1) were achieved in 3 L bioreactor. CONCLUSIONS With metabolic engineering and fermentation optimization practice, C. glutamicum 21850 (pEC-C-vio1) was able to produce violacein with both titer and productivity at the highest level ever reported. Due to advantages of mature C. glutamicum fermentation industry, this work has built basis for commercial production of violacein.
Collapse
Affiliation(s)
- Hongnian Sun
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034 People’s Republic of China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Bin Xiong
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Chunzhi Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034 People’s Republic of China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| |
Collapse
|
49
|
Nakayama M, Komiya S, Fujiwara K, Horisawa K, Doi N. In vitro selection of bispecific diabody fragments using covalent bicistronic DNA display. Biochem Biophys Res Commun 2016; 478:606-11. [PMID: 27473655 DOI: 10.1016/j.bbrc.2016.07.113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/25/2016] [Indexed: 12/25/2022]
Abstract
Bispecific antibodies with two different antigen-binding sites have been widely used for a variety of medical applications. The activity and stability of antibody fragments can be improved by in vitro evolution. Although the affinity and stability of small bispecific antibody fragments such as diabodies can be further optimized by in vitro display technologies, cell-free display of bispecific antibody fragments has not been reported. In this study, we applied a covalent bicistronic DNA display for the in vitro selection of heterodimeric diabodies. First, we confirmed the antigen-binding activities of a diabody synthesized by an in vitro transcription and translation system. However, when we performed DNA-display selection of a model diabody library in a proof-of-principle experiment, no enrichment of the diabody gene was observed, likely due to a low yield of the diabody heterodimer. To overcome this issue, we introduced cysteine residues at the VH-VL interface of the diabody heterodimer. Using the disulfide-stabilized diabodies, we successfully enriched the diabody gene from a model library. Our results indicate that the covalent bicistronic DNA display technique could be useful for improving the stability and affinity of bispecific diabody fragments.
Collapse
Affiliation(s)
- Masanao Nakayama
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Shoko Komiya
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Kenichi Horisawa
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan.
| |
Collapse
|
50
|
Nupur LNU, Vats A, Dhanda SK, Raghava GPS, Pinnaka AK, Kumar A. ProCarDB: a database of bacterial carotenoids. BMC Microbiol 2016; 16:96. [PMID: 27230105 PMCID: PMC4882832 DOI: 10.1186/s12866-016-0715-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 05/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids. Results Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.
Collapse
Affiliation(s)
- L N U Nupur
- Microbial Type Culture collection and Gene Bank (MTCC), Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
| | - Asheema Vats
- Infectious Diseases and Immunity, Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh, India
| | - Sandeep Kumar Dhanda
- Bioinformatics Centre, Council of Scientific and Industrial Research- Institute of Microbial Technology, Chandigarh, India
| | - Gajendra P S Raghava
- Bioinformatics Centre, Council of Scientific and Industrial Research- Institute of Microbial Technology, Chandigarh, India
| | - Anil Kumar Pinnaka
- Microbial Type Culture collection and Gene Bank (MTCC), Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39 A, 160036, Chandigarh, India.
| | - Ashwani Kumar
- Infectious Diseases and Immunity, Council of Scientific and Industrial Research, Institute of Microbial Technology, Sector 39 A, 160036, Chandigarh, India.
| |
Collapse
|