1
|
Guo L, Yang G. Pioneering DNA assembling techniques and their applications in eukaryotic microalgae. Biotechnol Adv 2024; 70:108301. [PMID: 38101551 DOI: 10.1016/j.biotechadv.2023.108301] [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: 09/27/2023] [Revised: 11/12/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Assembling DNA fragments is a fundamental manipulation of cloning microalgal genes and carrying out microalgal synthetic biological studies. From the earliest DNA recombination to current trait and metabolic pathway engineering, we are always accompanied by homology-based DNA assembling. The improvement and modification of pioneering DNA assembling techniques and the combinational applications of the available assembling techniques have diversified and complicated the literature environment and aggravated our identification of the core and pioneering methodologies. Identifying the core assembling methodologies and using them appropriately and flourishing them even are important for researchers. A group of microalgae have been evolving as the models for both industrial applications and biological studies. DNA assembling requires researchers to know the methods available and their improvements and evolvements. In this review, we summarized the pioneering (core; leading) DNA assembling techniques developed previously, extended these techniques to their modifications, improvements and their combinations, and highlighted their applications in eukaryotic microalgae. We predicted that the gene(s) will be assembled into a functional cluster (e.g., those involving in a metabolic pathway, and stacked on normal microalgal chromosomes, their artificial episomes and looming artificial chromosomes. It should be particularly pointed out that the techniques mentioned in this review are classified according to the strategy used to assemble the final construct.
Collapse
Affiliation(s)
- Li Guo
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China
| | - Guanpin Yang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, PR China; Institutes of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; MoE Laboratory of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, PR China; Key Laboratory of Marine Genetics and Breeding of Ministry of Education, Ocean University of China, Qingdao 266003, China.
| |
Collapse
|
2
|
Huang Y, Ye Z, Wan X, Yao G, Duan J, Liu J, Yao M, Sun X, Deng Z, Shen K, Jiang H, Liu T. Systematic Mining and Evaluation of the Sesquiterpene Skeletons as High Energy Aviation Fuel Molecules. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300889. [PMID: 37271925 PMCID: PMC10427387 DOI: 10.1002/advs.202300889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/26/2023] [Indexed: 06/06/2023]
Abstract
Sesquiterpenes have been identified as promising ingredients for aviation fuels due to their high energy density and combustion heat properties. Despite the characterization of numerous sesquiterpene structures, studies testing their performance properties and feasibility as fuels are scarce. In this study, 122 sesquiterpenoid skeleton compounds, obtained from existing literature reports, are tested using group contribution and gaussian quantum chemistry methods to assess their potential as high-energy aviation fuels. Seventeen sesquiterpene compounds exhibit good predictive performance and nine compounds are further selected for overproduction in yeast. Through fed-batch fermentation, all compounds achieve the highest reported titers to date. Subsequently, three representative products, pentalenene, presilphiperfol-1-ene, and α-farnesene, are selected, produced, purified in large quantities, and tested for use as potential fuels. The performance of pentalenene, presilphiperfol-1-ene, and their derivatives reveals favorable prospects as high-energy aviation fuels.
Collapse
Affiliation(s)
- Yanglei Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Ziling Ye
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Xiukun Wan
- State Key Laboratory of NBC Protection for CivilianBeijing102205China
| | - Ge Yao
- State Key Laboratory of NBC Protection for CivilianBeijing102205China
| | - Jingyu Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Jiajia Liu
- State Key Laboratory of NBC Protection for CivilianBeijing102205China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Frontier Technology Research InstituteTianjin UniversityTianjin301700China
| | - Xiang Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200030China
| | - Kun Shen
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Hui Jiang
- State Key Laboratory of NBC Protection for CivilianBeijing102205China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Hubei Engineering Laboratory for Synthetic MicrobiologyWuhan Institute of BiotechnologyWuhan430075China
| |
Collapse
|
3
|
Wu M, Gong DC, Yang Q, Zhang MQ, Mei YZ, Dai CC. Activation of Naringenin and Kaempferol through Pathway Refactoring in the Endophyte Phomopsis Liquidambaris. ACS Synth Biol 2021; 10:2030-2039. [PMID: 34251173 DOI: 10.1021/acssynbio.1c00205] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Abundant gene clusters of natural products are observed in the endophytic fungus Phomopsis liquidambaris; however, most of them are silent. Herein, a plug-and-play DNA assembly tool has been applied for flavonoid synthesis in P. liquidambaris. A shuttle plasmid was constructed based on S. cerevisiae, E. coli, and P. liquidambaris with screening markers URA, Amp, and hygR, respectively. Each fragment or cassette was successively assembled by overlap extension PCR with at least 40-50 bp homologous arms in S. cerevisiae for generating a new vector. Seven native promoters were screened by the DNA assembly based on the fluorescence intensity of the mCherry reporter gene in P. liquidambaris, and two of them were new promoters. The key enzyme chalcone synthase was the limiting step of the pathway. The naringenin and kaempferol pathways were refactored and activated with the titers of naringenin and kaempferol of 121.53 mg/L and 75.38 mg/L in P. liquidambaris using fed-batch fermentation, respectively. This study will be efficient and helpful for the biosynthesis of secondary metabolites.
Collapse
Affiliation(s)
- Mei Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province China
| | - Da-Chun Gong
- China Key Laboratory of Light Industry Functional Yeast, Three Gorges University, Yichang, 443000, Hubei Province China
| | - Qian Yang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province China
| | - Meng-Qian Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province China
| | - Yan-Zhen Mei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, Jiangsu Province China
| |
Collapse
|
4
|
Zhu Y, Cao L. Targeted Integration of Complex Genetic Elements at Multi-Copy Loci by Golden Gate Assembly. Methods Mol Biol 2021; 2196:143-151. [PMID: 32889718 DOI: 10.1007/978-1-0716-0868-5_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Budding yeast Saccharomyces cerevisiae has become a model eukaryotic microorganism for targeted genomic manipulation due to its efficient homologous recombination. A few genomic loci, including rDNA, Delta, and Ty1, can be utilized to introduce variable copies of genetic elements into the yeast genome. Here we describe a method that combines in vitro Golden Gate Assembly to assemble one or a complex genetic element in an orderly manner and then integrate it into predetermined multi-copy loci through homologous recombination. Different transformants may contain different copy numbers, which allows the selection of desired levels of target gene expression.
Collapse
Affiliation(s)
- Yixuan Zhu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Limin Cao
- College of Life Sciences, Capital Normal University, Beijing, China.
| |
Collapse
|
5
|
Damalas SG, Batianis C, Martin‐Pascual M, de Lorenzo V, Martins dos Santos VAP. SEVA 3.1: enabling interoperability of DNA assembly among the SEVA, BioBricks and Type IIS restriction enzyme standards. Microb Biotechnol 2020; 13:1793-1806. [PMID: 32710525 PMCID: PMC7533339 DOI: 10.1111/1751-7915.13609] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/22/2020] [Accepted: 05/18/2020] [Indexed: 01/15/2023] Open
Abstract
Robust synthetic biology applications rely heavily on the design and assembly of DNA parts with specific functionalities based on engineering principles. However, the assembly standards adopted by different communities vary considerably, thus limiting the interoperability of parts, vectors and methods. We hereby introduce the SEVA 3.1 platform consisting of the SEVA 3.1 vectors and the Golden Gate-based 'SevaBrick Assembly'. This platform enables the convergence of standard processes between the SEVA platform, the BioBricks and the Type IIs-mediated DNA assemblies to reduce complexity and optimize compatibility between parts and methods. It features a wide library of cloning vectors along with a core set of standard SevaBrick primers that allow multipart assembly and exchange of short functional genetic elements (promoters, RBSs) with minimal cloning and design effort. As proof of concept, we constructed, among others, multiple sfGFP expression vectors under the control of eight RBSs, eight promoters and four origins of replication as well as an inducible four-gene operon expressing the biosynthetic genes for the black pigment proviolacein. To demonstrate the interoperability of the SEVA 3.1 vectors, all constructs were characterized in both Pseudomonas putida and Escherichia coli. In summary, the SEVA 3.1 platform optimizes compatibility and modularity of inserts and backbones with a cost- and time-friendly DNA assembly method, substantially expanding the toolbox for successful synthetic biology applications in Gram-negative bacteria.
Collapse
Affiliation(s)
- Stamatios G. Damalas
- Laboratory of Systems and Synthetic BiologyWageningen & Research UniversityStippeneng 4Wageningen6708 WEThe Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic BiologyWageningen & Research UniversityStippeneng 4Wageningen6708 WEThe Netherlands
| | - Maria Martin‐Pascual
- Laboratory of Systems and Synthetic BiologyWageningen & Research UniversityStippeneng 4Wageningen6708 WEThe Netherlands
| | - Victor de Lorenzo
- Systems Biology ProgramNational Center of Biotechnology − CSICMadrid28049Spain
| | - Vitor A. P. Martins dos Santos
- Laboratory of Systems and Synthetic BiologyWageningen & Research UniversityStippeneng 4Wageningen6708 WEThe Netherlands
- Lifeglimmer GmbHMarkelstrasse 38Berlin12163Germany
| |
Collapse
|
6
|
Kayacan Y, Griffiths A, Wendland J. A script for initiating molecular biology studies with non-conventional yeasts based on Saccharomycopsis schoenii. Microbiol Res 2019; 229:126342. [PMID: 31536874 DOI: 10.1016/j.micres.2019.126342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023]
Abstract
Non-conventional yeasts (NCYs), i.e. all yeasts other than Saccharomyces cerevisiae, are emerging as novel production strains and gain more and more attention to exploit their unique properties. Yet, these yeasts can hardly compete against the advanced methodology and genetic tool kit available for exploiting and engineering S. cerevisiae. Currently, for many NCYs one has to start from scratch to initiate molecular genetic manipulations, which is often time consuming and not straight-forward. More so because utilization of S. cerevisiae tools based on short-flank mediated homologous recombination or plasmid biology are not readily applicable in NCYs. Here we present a script with discrete steps that will lead to the development of a basic and expandable molecular toolkit for ascomycetous NCYs and will allow genetic engineering of novel platform strains. For toolkit development the highly efficient in vivo recombination efficiency of S. cerevisiae is utilized in the generation and initial testing of tools. The basic toolkit includes promoters, reporter genes, selectable markers based on dominant antibiotic resistance genes and the generation of long-flanking homology disruption cassettes. The advantage of having pretested molecular tools that function in a heterologous host facilitate NCY strain manipulations. We demonstrate the usefulness of this script on Saccharomycopsis schoenii, a predator yeast with useful properties in fermentation and fungal biocontrol.
Collapse
Affiliation(s)
- Yeseren Kayacan
- Vrije Universiteit Brussel, Functional Yeast Genomics, BE-1050 Brussels, Belgium
| | - Adam Griffiths
- Vrije Universiteit Brussel, Functional Yeast Genomics, BE-1050 Brussels, Belgium
| | - Jürgen Wendland
- Hochschule Geisenheim University, Department of Microbiology and Biochemistry, von-Lade-Strasse 1, D-65366 Geisenheim, Germany; Vrije Universiteit Brussel, Functional Yeast Genomics, BE-1050 Brussels, Belgium.
| |
Collapse
|
7
|
Designing with living systems in the synthetic yeast project. Nat Commun 2018; 9:2950. [PMID: 30054478 PMCID: PMC6063962 DOI: 10.1038/s41467-018-05332-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 06/28/2018] [Indexed: 11/08/2022] Open
Abstract
Synthetic biology is challenged by the complexity and the unpredictability of living systems. While one response to this complexity involves simplifying cells to create more fully specified systems, another approach utilizes directed evolution, releasing some control and using unpredictable change to achieve design goals. Here we discuss SCRaMbLE, employed in the synthetic yeast project, as an example of synthetic biology design through working with living systems. SCRaMbLE is a designed tool without being a design tool, harnessing the activities of the yeast rather than relying entirely on scientists’ deliberate choices. We suggest that directed evolution at the level of the whole organism allows scientists and microorganisms to “collaborate” to achieve design goals, suggesting new directions for synthetic biology. Synthetic biology often views the organism as a chassis into which a circuit can be inserted. Here the authors explore the idea of the organism as a core aspect of design, aiding researchers in navigating the genetic space opened up by SCRaMbLE.
Collapse
|
8
|
An automated Design-Build-Test-Learn pipeline for enhanced microbial production of fine chemicals. Commun Biol 2018; 1:66. [PMID: 30271948 PMCID: PMC6123781 DOI: 10.1038/s42003-018-0076-9] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/10/2018] [Indexed: 12/15/2022] Open
Abstract
The microbial production of fine chemicals provides a promising biosustainable manufacturing solution that has led to the successful production of a growing catalog of natural products and high-value chemicals. However, development at industrial levels has been hindered by the large resource investments required. Here we present an integrated Design–Build-Test–Learn (DBTL) pipeline for the discovery and optimization of biosynthetic pathways, which is designed to be compound agnostic and automated throughout. We initially applied the pipeline for the production of the flavonoid (2S)-pinocembrin in Escherichia coli, to demonstrate rapid iterative DBTL cycling with automation at every stage. In this case, application of two DBTL cycles successfully established a production pathway improved by 500-fold, with competitive titers up to 88 mg L−1. The further application of the pipeline to optimize an alkaloids pathway demonstrates how it could facilitate the rapid optimization of microbial strains for production of any chemical compound of interest. Pablo Carbonell et al. present an automated pipeline for the discovery and optimization of biosynthetic pathways for microbial production of fine chemicals. They apply their pipeline to the production of the flavonoid (2S)-pinocembrin in Escherichia coli and show improvement of the pathway by 500-fold.
Collapse
|
9
|
Shepherd ES, DeLoache WC, Pruss KM, Whitaker WR, Sonnenburg JL. An exclusive metabolic niche enables strain engraftment in the gut microbiota. Nature 2018; 557:434-438. [PMID: 29743671 PMCID: PMC6126907 DOI: 10.1038/s41586-018-0092-4] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 03/23/2018] [Indexed: 11/09/2022]
Abstract
The dense microbial ecosystem in the gut is intimately connected to numerous facets of human biology, and manipulation of the gut microbiota has broad implications for human health. In the absence of profound perturbation, the bacterial strains that reside within an individual are mostly stable over time 1 . By contrast, the fate of exogenous commensal and probiotic strains applied to an established microbiota is variable, generally unpredictable and greatly influenced by the background microbiota2,3. Therefore, analysis of the factors that govern strain engraftment and abundance is of critical importance to the emerging field of microbiome reprogramming. Here we generate an exclusive metabolic niche in mice via administration of a marine polysaccharide, porphyran, and an exogenous Bacteroides strain harbouring a rare gene cluster for porphyran utilization. Privileged nutrient access enables reliable engraftment of the exogenous strain at predictable abundances in mice harbouring diverse communities of gut microbes. This targeted dietary support is sufficient to overcome priority exclusion by an isogenic strain 4 , and enables strain replacement. We demonstrate transfer of the 60-kb porphyran utilization locus into a naive strain of Bacteroides, and show finely tuned control of strain abundance in the mouse gut across multiple orders of magnitude by varying porphyran dosage. Finally, we show that this system enables the introduction of a new strain into the colonic crypt ecosystem. These data highlight the influence of nutrient availability in shaping microbiota membership, expand the ability to perform a broad spectrum of investigations in the context of a complex microbiota, and have implications for cell-based therapeutic strategies in the gut.
Collapse
Affiliation(s)
- Elizabeth Stanley Shepherd
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
- Novome Biotechnologies, South San Francisco, CA, USA
| | | | - Kali M Pruss
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
10
|
Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications. PLoS One 2017; 12:e0177234. [PMID: 28531174 PMCID: PMC5439662 DOI: 10.1371/journal.pone.0177234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.
Collapse
|