51
|
Recent Advances in Genome Editing Tools in Medical Mycology Research. J Fungi (Basel) 2021; 7:jof7040257. [PMID: 33808382 PMCID: PMC8067129 DOI: 10.3390/jof7040257] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
Manipulating fungal genomes is an important tool to understand the function of target genes, pathobiology of fungal infections, virulence potential, and pathogenicity of medically important fungi, and to develop novel diagnostics and therapeutic targets. Here, we provide an overview of recent advances in genetic manipulation techniques used in the field of medical mycology. Fungi use several strategies to cope with stress and adapt themselves against environmental effectors. For instance, mutations in the 14 alpha-demethylase gene may result in azole resistance in Aspergillusfumigatus strains and shield them against fungicide's effects. Over the past few decades, several genome editing methods have been introduced for genetic manipulations in pathogenic fungi. Application of restriction enzymes to target and cut a double-stranded DNA in a pre-defined sequence was the first technique used for cloning in Aspergillus and Candida. Genome editing technologies, including zinc-finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), have been also used to engineer a double-stranded DNA molecule. As a result, TALENs were considered more practical to identify single nucleotide polymorphisms. Recently, Class 2 type II Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 technology has emerged as a more useful tool for genome manipulation in fungal research.
Collapse
|
52
|
Singh R, Chandel S, Ghosh A, Dey D, Chakravarti R, Roy S, Ravichandiran V, Ghosh D. Application of CRISPR/Cas System in the Metabolic Engineering of Small Molecules. Mol Biotechnol 2021; 63:459-476. [PMID: 33774733 DOI: 10.1007/s12033-021-00310-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/14/2021] [Indexed: 12/18/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas protein technology area is rapidly growing technique for genome editing and modulation of transcription of several microbes. Successful engineering in microbes requires an emphasis on the aspect of efficiency and targeted aiming, which can be employed using CRISPR/Cas system. Hence, this type of system is used to modify the genome of several microbes such as yeast and bacteria. In recent years, CRISPR/Cas systems have been chosen for metabolic engineering in microbes due to their specificity, orthogonality, and efficacy. Therefore, we need to review the scheme which was acquired for the execution of the CRISPR/Cas system for the modification and metabolic engineering in yeast and bacteria. In this review, we highlighted the application of the CRISPR/Cas system which has been used for the production of small molecules in the microbial system that is chemically and biologically important.
Collapse
Affiliation(s)
- Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Shivani Chandel
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Arijit Ghosh
- Department of Chemistry, University of Calcutta, Kolkata, 700009, India
| | - Dhritiman Dey
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Syamal Roy
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - V Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India
| | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research, Kolkata, 700054, India.
| |
Collapse
|
53
|
Developing GDi-CRISPR System for Multi-copy Integration in Saccharomyces cerevisiae. Appl Biochem Biotechnol 2021; 193:2379-2388. [PMID: 33660219 DOI: 10.1007/s12010-021-03532-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/26/2021] [Indexed: 10/22/2022]
Abstract
In recent years, Saccharomyces cerevisiae has been widely used in the production of biofuels and value-added chemicals. To stably express the target products, it is necessary to integrate multiple target genes into the chromosome of S. cerevisiae. CRISPR multi-copy integration technology relying on delta sites has been developed, but it often requires the help of high-throughput screening or resistance markers, resulting in non-replicability and high cost. This study aims to develop a low-cost and easy-to-use multi-copy integration tool in S. cerevisiae. Firstly, twenty-one Cas proteins from different microorganisms were tested in S. cerevisiae to find the functional Cas proteins with optimal cleavage ability. Results showed that eight Cas proteins can complete gene editing. However, most of the transformants have low copy numbers, which may be caused by high cutting efficiency exceeding the repair rate. Therefore, the effect of donor translocation order was further investigated. Results showed that 4 copies were obtained by donor first translocation. Then, the gene drive delta site integration system by the CRISPR system (GDi-CRISPR) was developed by combining gene drive principle and CRISPR system. To be clear, the gRNA was put into donor fragments. Then, both of them were integrated into the genome, which can drive further cutting and repair due to increasing number of gRNA. Instead of high-throughput screening or resistance pressure, 6 copies were obtained in only 5-6 days using the GDi-CRISPR system. It is expected to further advance the development of S. cerevisiae multi-copy integration tools.
Collapse
|
54
|
Baek S, Utomo JC, Lee JY, Dalal K, Yoon YJ, Ro DK. The yeast platform engineered for synthetic gRNA-landing pads enables multiple gene integrations by a single gRNA/Cas9 system. Metab Eng 2021; 64:111-121. [PMID: 33549837 DOI: 10.1016/j.ymben.2021.01.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 12/28/2020] [Accepted: 01/30/2021] [Indexed: 12/25/2022]
Abstract
Saccharomyces cerevisiae is a versatile microbial platform to build synthetic metabolic pathways for production of diverse chemicals. To expedite the construction of complex metabolic pathways by multiplex CRISPR-Cas9 genome-edit, eight desirable intergenic loci, located adjacent to highly expressed genes selected from top 100 expressers, were identified and fully characterized for three criteria after integrating green fluorescent protein (GFP) gene - CRISPR-mediated GFP integration efficiency, expression competency assessed by levels of GFP fluorescence, and assessing growth rates of GFP integrated strains. Five best performing intergenic loci were selected to build a multiplex CRISPR platform, and a synthetic 23-bp DNA comprised of 20-bp synthetic DNA with a protospacer adjacent motif (PAM) was integrated into the five loci using CRISPR-Cas9 in a sequential manner. This process resulted in five different yeast strains harbouring 1-5 synthetic gRNA-binding sites in their genomes. Using these pre-engineered yeast strains, simultaneous integrations of 2-, 3-, 4-, or 5-genes to the targeted loci were demonstrated with efficiencies from 85% to 98% using beet pigment betalain (3-gene pathway), hygromycin and geneticin resistance markers. Integrations of the multiple, foreign genes in the targeted loci with 100% precision were validated by genotyping. Finally, we further developed the strain to have 6th synthetic gRNA-binding site, and the resulting yeast strain was used to generate a yeast strain producing a sesquiterpene lactone, kauniolide by simultaneous 6-gene integrations. This study demonstrates the effectiveness of a single gRNA-mediated CRISPR platform to build complex metabolic pathways in yeast.
Collapse
Affiliation(s)
- Sihyun Baek
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | | | - Ji Young Lee
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Kunal Dalal
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada
| | - Yeo Joon Yoon
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dae-Kyun Ro
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N1N4, Canada.
| |
Collapse
|
55
|
Qi M, Zhang B, Jiang L, Xu S, Dong C, Du YL, Zhou Z, Huang L, Xu Z, Lian J. PCR & Go: A Pre-installed Expression Chassis for Facile Integration of Multi-Gene Biosynthetic Pathways. Front Bioeng Biotechnol 2021; 8:613771. [PMID: 33520963 PMCID: PMC7841387 DOI: 10.3389/fbioe.2020.613771] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 12/07/2020] [Indexed: 11/29/2022] Open
Abstract
The introduction of multi-gene metabolic pathways is generally the first step for the construction of microbial cell factories and plays an essential role in metabolic engineering and synthetic biology. Here, we developed a “PCR & Go” system for facile integration and assembly of multi-gene pathways into the chromosome of Saccharomyces cerevisiae. The core component of the “PCR & Go” system was an expression chassis, where eight promoter/terminator pairs were pre-installed into the yeast chromosome and PCR amplified gene fragments could be inserted directly for functional expression. In combination with the CRISPR/Cas9 system and a gRNA plasmid library, the β-carotene (three genes), zeaxanthin (four genes), and astaxanthin (five genes) biosynthetic pathways were integrated and assembled into the yeast genome with an efficiency of ~93, ~85, and 69%, respectively, using PCR amplified gene fragments with ~40 bp homology arms in a single step. Therefore, the “PCR & Go” system can be used for fast construction of yeast cell factories harboring multi-gene pathways with high efficiency and flexibility.
Collapse
Affiliation(s)
- Mingming Qi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bei Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Saijuan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Yi-Ling Du
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhan Zhou
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| |
Collapse
|
56
|
Navale GR, Dharne MS, Shinde SS. Metabolic engineering and synthetic biology for isoprenoid production in Escherichia coli and Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2021; 105:457-475. [PMID: 33394155 DOI: 10.1007/s00253-020-11040-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 12/29/2022]
Abstract
Isoprenoids, often called terpenoids, are the most abundant and highly diverse family of natural organic compounds. In plants, they play a distinct role in the form of photosynthetic pigments, hormones, electron carrier, structural components of membrane, and defence. Many isoprenoids have useful applications in the pharmaceutical, nutraceutical, and chemical industries. They are synthesized by various isoprenoid synthase enzymes by several consecutive steps. Recent advancement in metabolic engineering and synthetic biology has enabled the production of these isoprenoids in the heterologous host systems like Escherichia coli and Saccharomyces cerevisiae. Both heterologous systems have been engineered for large-scale production of value-added isoprenoids. This review article will provide the detailed description of various approaches used for engineering of methyl-D-erythritol-4-phosphate (MEP) and mevalonate (MVA) pathway for synthesizing isoprene units (C5) and ultimate production of diverse isoprenoids. The review particularly highlighted the efforts taken for the production of C5-C20 isoprenoids by metabolic engineering techniques in E. coli and S. cerevisiae over a decade. The challenges and strategies are also discussed in detail for scale-up and engineering of isoprenoids in the heterologous host systems.Key points• Isoprenoids are beneficial and valuable natural products.• E. coli and S. cerevisiae are the promising host for isoprenoid biosynthesis.• Emerging techniques in synthetic biology enabled the improved production.• Need to expand the catalogue and scale-up of un-engineered isoprenoids. Metabolic engineering and synthetic biology for isoprenoid production in Escherichia coli and Saccharomyces cerevisiae.
Collapse
Affiliation(s)
- Govinda R Navale
- NCIM Resource Centre, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 001, India
| | - Mahesh S Dharne
- NCIM Resource Centre, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 001, India.
| | - Sandip S Shinde
- NCIM Resource Centre, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India. .,Department Industrial and Chemical Engineering, Institute of Chemical Technology Mumbai Marathwada Campus, Jalna, 431213, India.
| |
Collapse
|
57
|
Utomo JC, Hodgins CL, Ro DK. Multiplex Genome Editing in Yeast by CRISPR/Cas9 - A Potent and Agile Tool to Reconstruct Complex Metabolic Pathways. FRONTIERS IN PLANT SCIENCE 2021; 12:719148. [PMID: 34421973 PMCID: PMC8374951 DOI: 10.3389/fpls.2021.719148] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/14/2021] [Indexed: 05/22/2023]
Abstract
Numerous important pharmaceuticals and nutraceuticals originate from plant specialized metabolites, most of which are synthesized via complex biosynthetic pathways. The elucidation of these pathways is critical for the applicable uses of these compounds. Although the rapid progress of the omics technology has revolutionized the identification of candidate genes involved in these pathways, the functional characterization of these genes remains a major bottleneck. Baker's yeast (Saccharomyces cerevisiae) has been used as a microbial platform for characterizing newly discovered metabolic genes in plant specialized metabolism. Using yeast for the investigation of numerous plant enzymes is a streamlined process because of yeast's efficient transformation, limited endogenous specialized metabolism, partially sharing its primary metabolism with plants, and its capability of post-translational modification. Despite these advantages, reconstructing complex plant biosynthetic pathways in yeast can be time intensive. Since its discovery, CRISPR/Cas9 has greatly stimulated metabolic engineering in yeast. Yeast is a popular system for genome editing due to its efficient homology-directed repair mechanism, which allows precise integration of heterologous genes into its genome. One practical use of CRISPR/Cas9 in yeast is multiplex genome editing aimed at reconstructing complex metabolic pathways. This system has the capability of integrating multiple genes of interest in a single transformation, simplifying the reconstruction of complex pathways. As plant specialized metabolites usually have complex multigene biosynthetic pathways, the multiplex CRISPR/Cas9 system in yeast is suited well for functional genomics research in plant specialized metabolism. Here, we review the most advanced methods to achieve efficient multiplex CRISPR/Cas9 editing in yeast. We will also discuss how this powerful tool has been applied to benefit the study of plant specialized metabolism.
Collapse
|
58
|
Strucko T, Lisby M, Mortensen UH. DNA Double-Strand Break-Induced Gene Amplification in Yeast. Methods Mol Biol 2021; 2153:239-252. [PMID: 32840784 DOI: 10.1007/978-1-0716-0644-5_17] [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] [Indexed: 06/11/2023]
Abstract
Precise control of the gene copy number in the model yeast Saccharomyces cerevisiae may facilitate elucidation of enzyme functions or, in cell factory design, can be used to optimize production of proteins and metabolites. Currently, available methods can provide high gene-expression levels but fail to achieve accurate gene dosage. Moreover, strains generated using these methods often suffer from genetic instability resulting in loss of gene copies during prolonged cultivation. Here we present a method, CASCADE, which enables construction of strains with defined gene copy number. With our present system, gene(s) of interest can be amplified up to nine copies, but the upper copy limit of the system can be expanded. Importantly, the resulting strains can be stably propagated in selection-free media.
Collapse
Affiliation(s)
- Tomas Strucko
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Uffe Hasbro Mortensen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.
| |
Collapse
|
59
|
Rainha J, Rodrigues JL, Rodrigues LR. CRISPR-Cas9: A Powerful Tool to Efficiently Engineer Saccharomyces cerevisiae. Life (Basel) 2020; 11:13. [PMID: 33375364 PMCID: PMC7823794 DOI: 10.3390/life11010013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/23/2020] [Accepted: 12/24/2020] [Indexed: 12/27/2022] Open
Abstract
Saccharomyces cerevisiae has been for a long time a common model for fundamental biological studies and a popular biotechnological engineering platform to produce chemicals, fuels, and pharmaceuticals due to its peculiar characteristics. Both lines of research require an effective editing of the native genetic elements or the inclusion of heterologous pathways into the yeast genome. Although S. cerevisiae is a well-known host with several molecular biology tools available, a more precise tool is still needed. The clustered, regularly interspaced, short palindromic repeats-associated Cas9 (CRISPR-Cas9) system is a current, widespread genome editing tool. The implementation of a reprogrammable, precise, and specific method, such as CRISPR-Cas9, to edit the S. cerevisiae genome has revolutionized laboratory practices. Herein, we describe and discuss some applications of the CRISPR-Cas9 system in S. cerevisiae from simple gene knockouts to more complex processes such as artificial heterologous pathway integration, transcriptional regulation, or tolerance engineering.
Collapse
Affiliation(s)
| | | | - Lígia R. Rodrigues
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (J.R.); (J.L.R.)
| |
Collapse
|
60
|
Meng J, Qiu Y, Shi S. CRISPR/Cas9 Systems for the Development of Saccharomyces cerevisiae Cell Factories. Front Bioeng Biotechnol 2020; 8:594347. [PMID: 33330425 PMCID: PMC7710542 DOI: 10.3389/fbioe.2020.594347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/19/2020] [Indexed: 01/09/2023] Open
Abstract
Synthetic yeast cell factories provide a remarkable solution for the sustainable supply of a range of products, ranging from large-scale industrial chemicals to high-value pharmaceutical compounds. Synthetic biology is a field in which metabolic pathways are intensively studied and engineered. The clustered, regularly interspaced, short, palindromic repeat-associated (CRISPR)/CRISPR-associated protein 9 (Cas9) technology has emerged as the state-of-the-art gene editing technique for synthetic biology. Recently, the use of different CRISPR/Cas9 systems has been extended to the field of yeast engineering for single-nucleotide resolution editing, multiple-gene editing, transcriptional regulation, and genome-scale modifications. Such advancing systems have led to accelerated microbial engineering involving less labor and time and also enhanced the understanding of cellular genetics and physiology. This review provides a brief overview of the latest research progress and the use of CRISPR/Cas9 systems in genetic manipulation, with a focus on the applications of Saccharomyces cerevisiae cell factory engineering.
Collapse
Affiliation(s)
- Jie Meng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yue Qiu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| |
Collapse
|
61
|
Qin N, Li L, Ji X, Li X, Zhang Y, Larsson C, Chen Y, Nielsen J, Liu Z. Rewiring Central Carbon Metabolism Ensures Increased Provision of Acetyl-CoA and NADPH Required for 3-OH-Propionic Acid Production. ACS Synth Biol 2020; 9:3236-3244. [PMID: 33186034 DOI: 10.1021/acssynbio.0c00264] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The central carbon metabolite acetyl-CoA and the cofactor NADPH are important for the synthesis of a wide array of biobased products. Here, we constructed a platform yeast strain for improved provision of acetyl-CoA and NADPH, and used the production of 3-hydroxypropionic acid (3-HP) as a case study. We first demonstrated that the integration of phosphoketolase and phosphotransacetylase improved 3-HP production by 41.9% and decreased glycerol production by 48.1% compared with that of the control strain. Then, to direct more carbon flux toward the pentose phosphate pathway, we reduced the expression of phosphoglucose isomerase by replacing its native promoter with a weaker promoter, and increased the expression of glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase by replacing their native promoters with stronger promoters. This further improved 3-HP production by 26.4%. Furthermore, to increase the NADPH supply we overexpressed cytosolic aldehyde dehydrogenase, and improved 3-HP production by another 10.5%. Together with optimizing enzyme expression of acetyl-CoA carboxylase and malonyl-CoA reductase, the final strain is able to produce 3-HP with a final titer of 864.5 mg/L, which is a more than 24-fold improvement compared with that of the starting strain. Our strategy combines the PK pathway with the oxidative pentose phosphate pathway for the efficient provision of acetyl-CoA and NADPH, which provides both a higher theoretical yield and overall yield than the reported yeast-based 3-HP production strategies via the malonyl-CoA reductase-dependent pathway and sheds light on the construction of efficient platform cell factories for other products.
Collapse
Affiliation(s)
- Ning Qin
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Lingyun Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Xu Ji
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden
| | - Yiming Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Christer Larsson
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, 100029 Beijing, China
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296 Gothenburg, Sweden
- BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen, Denmark
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, 100029 Beijing, China
| |
Collapse
|
62
|
Nishida K, Kondo A. CRISPR-derived genome editing technologies for metabolic engineering. Metab Eng 2020; 63:141-147. [PMID: 33307189 DOI: 10.1016/j.ymben.2020.12.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022]
Abstract
In metabolic engineering, genome editing tools make it much easier to discover and evaluate relevant genes and pathways and construct strains. Clustered regularly interspaced palindromic repeats (CRISPR)-associated (Cas) systems now have become the first choice for genome engineering in many organisms includingindustrially relevant ones. Targeted DNA cleavage by CRISPR-Cas provides variousgenome engineering modes such as indels, replacements, large deletions, knock-in and chromosomal rearrangements, while host-dependent differences in repair pathways need to be considered. The versatility of the CRISPR system has given rise to derivative technologies that complement nuclease-based editing, which causes cytotoxicity especially in microorganisms. Deaminase-mediated base editing installs targeted point mutations with much less toxicity. CRISPRi and CRISPRa can temporarily control gene expression without changing the genomic sequence. Multiplex, combinatorial and large scale editing are made possible by streamlined design and construction of gRNA libraries to further accelerates comprehensive discovery, evaluation and building of metabolic pathways. This review summarizes the technical basis and recent advances in CRISPR-related genome editing tools applied for metabolic engineering purposes, with representative examples of industrially relevant eukaryotic and prokaryotic organisms.
Collapse
Affiliation(s)
- Keiji Nishida
- Engineering Biology Research Center, Kobe University, Japan; Graduate School of Science, Technology and Innovation, Kobe University, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, Japan; Graduate School of Science, Technology and Innovation, Kobe University, Japan.
| |
Collapse
|
63
|
Li G, Li H, Lyu Y, Zeng W, Zhou J. Enhanced Biosynthesis of Dihydromyricetin in Saccharomyces cerevisiae by Coexpression of Multiple Hydroxylases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14221-14229. [PMID: 33205970 DOI: 10.1021/acs.jafc.0c05261] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dihydromyricetin (DHM) is a traditional plant-extracted flavonoid with some health benefits. This study aimed to metabolically engineer the strains for DHM bioproduction. Two strains of BK-11 and BQ-21 were integrated with flavonoid 3-hydroxylase (F3H) or both F3H and flavonoid 3'-hydroxylase (F3'H). The resulting strains have expressed the enzymes of GmCPR and SlF3'5'H, and then, the promoters of INO1p and TDH1p were used to enhance further the DHM production from naringenin in Saccharomyces cerevisiae. Through multiple-copy integration, 709.6 mg/L DHM was obtained by adding 2.5 g/L naringenin in a 5 L bioreactor, implying that the synergistic effect between F3'H and flavonoid 3'5'-hydroxylase is likely to promote the DHM production. An yield of 246.4 mg/L DHM was obtained from glucose by deleting genes for branch pathways and integrating PhCHS, MsCHI, Pc4CL, and FjTAL. To our knowledge, this is the highest production reported for the de novo biosynthesis of DHM.
Collapse
Affiliation(s)
- Guangjian Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Hongbiao Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yunbin Lyu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| |
Collapse
|
64
|
Malcı K, Walls LE, Rios-Solis L. Multiplex Genome Engineering Methods for Yeast Cell Factory Development. Front Bioeng Biotechnol 2020; 8:589468. [PMID: 33195154 PMCID: PMC7658401 DOI: 10.3389/fbioe.2020.589468] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
As biotechnological applications of synthetic biology tools including multiplex genome engineering are expanding rapidly, the construction of strategically designed yeast cell factories becomes increasingly possible. This is largely due to recent advancements in genome editing methods like CRISPR/Cas tech and high-throughput omics tools. The model organism, baker's yeast (Saccharomyces cerevisiae) is an important synthetic biology chassis for high-value metabolite production. Multiplex genome engineering approaches can expedite the construction and fine tuning of effective heterologous pathways in yeast cell factories. Numerous multiplex genome editing techniques have emerged to capitalize on this recently. This review focuses on recent advancements in such tools, such as delta integration and rDNA cluster integration coupled with CRISPR-Cas tools to greatly enhance multi-integration efficiency. Examples of pre-placed gate systems which are an innovative alternative approach for multi-copy gene integration were also reviewed. In addition to multiple integration studies, multiplexing of alternative genome editing methods are also discussed. Finally, multiplex genome editing studies involving non-conventional yeasts and the importance of automation for efficient cell factory design and construction are considered. Coupling the CRISPR/Cas system with traditional yeast multiplex genome integration or donor DNA delivery methods expedites strain development through increased efficiency and accuracy. Novel approaches such as pre-placing synthetic sequences in the genome along with improved bioinformatics tools and automation technologies have the potential to further streamline the strain development process. In addition, the techniques discussed to engineer S. cerevisiae, can be adapted for use in other industrially important yeast species for cell factory development.
Collapse
Affiliation(s)
- Koray Malcı
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
| | - Laura E Walls
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
| | - Leonardo Rios-Solis
- Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh, United Kingdom.,Centre for Synthetic and Systems Biology (SynthSys), The University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
65
|
Li H, Gao S, Zhang S, Zeng W, Zhou J. Effects of metabolic pathway gene copy numbers on the biosynthesis of (2S)-naringenin in Saccharomyces cerevisiae. J Biotechnol 2020; 325:119-127. [PMID: 33186660 DOI: 10.1016/j.jbiotec.2020.11.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 12/16/2022]
Abstract
Flavonoids have notable biological activities and have been widely used in the medicinal and chemical industries. However, single-copy integration of heterologous pathway genes limits the production of flavonoids. In this work, we designed and constructed single-step integration of multiple flavonoid (2S)-naringenin biosynthetic pathway genes in S. cerevisiae. The efficiency of the naringenin metabolic pathway gene integration into the rDNA site reached 93.7%. Subsequently, we used a high titer p-coumaric acid strain as a chassis, which eliminated feedback inhibition of tyrosine and downregulated the competitive pathway. The results indicated that increasing the supply of p-coumaric acid was effective for naringenin production. We additionally optimized the amount of donor DNA. The optimum strain produced 149.8 mg/L of (2S)-naringenin. The multi-copy integration of flavonoid pathway genes effectively improved (2S)-naringenin production in S. cerevisiae. We further analyzed the copy numbers and expression levels of essential genes (4CL and CHS) in the (2S)-naringenin metabolic pathway by qPCR. Higher copy numbers of the (2S)-naringenin metabolic pathway genes were associated with greater 4CL and CHS transcription, and the efficiency of naringenin production was higher. Therefore, multi-copy integration of genes in the (2S)-naringenin metabolic pathway was imperative in rewiring p-coumaric acid flux to enhance flavonoid production.
Collapse
Affiliation(s)
- Hongbiao Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Song Gao
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Siqi Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingwen Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
| |
Collapse
|
66
|
Zhao D, Zhu X, Zhou H, Sun N, Wang T, Bi C, Zhang X. CRISPR-based metabolic pathway engineering. Metab Eng 2020; 63:148-159. [PMID: 33152516 DOI: 10.1016/j.ymben.2020.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/27/2022]
Abstract
A highly effective metabolic pathway is the key for an efficient cell factory. However, the engineered homologous or heterologous multi-gene pathway may be unbalanced, inefficient and causing the accumulation of potentially toxic intermediates. Therefore, pathways must be constructed optimally to minimize these negative effects and maximize catalytic efficiency. With the development of CRISPR technology, some of the problems of previous pathway engineering and genome editing techniques were resolved, providing higher efficiency, lower cost, and easily customizable targets. Moreover, CRISPR was demonstrated as robust and effective in various organisms including both prokaryotes and eukaryotes. In recent years, researchers in the field of metabolic engineering and synthetic biology have exploited various CRISPR-based pathway engineering approaches, which are both effective and convenient, as well as valuable from a theoretical standpoint. In this review, we systematically summarize novel pathway engineering techniques and strategies based on CRISPR nucleases system, CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa), including figures and descriptions for easy understanding, with the aim to facilitate their broader application among fellow researchers.
Collapse
Affiliation(s)
- Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Hang Zhou
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Naxin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ting Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| |
Collapse
|
67
|
Hassan JU, Kaleem I, Rasool A, Xu K, Adnan Tahir R, Lv B, Li C. Engineered Saccharomyces cerevisiae for the de novo synthesis of the aroma compound longifolene. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2020.115799] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
68
|
López J, Bustos D, Camilo C, Arenas N, Saa PA, Agosin E. Engineering Saccharomyces cerevisiae for the Overproduction of β-Ionone and Its Precursor β-Carotene. Front Bioeng Biotechnol 2020; 8:578793. [PMID: 33102463 PMCID: PMC7556307 DOI: 10.3389/fbioe.2020.578793] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/08/2020] [Indexed: 11/30/2022] Open
Abstract
β-ionone is a commercially attractive industrial fragrance produced naturally from the cleavage of the pigment β-carotene in plants. While the production of this ionone is typically performed using chemical synthesis, environmentally friendly and consumer-oriented biotechnological production is gaining increasing attention. A convenient cell factory to address this demand is the yeast Saccharomyces cerevisiae. However, current β-ionone titers and yields are insufficient for commercial bioproduction. In this work, we optimized S. cerevisiae for the accumulation of high amounts of β-carotene and its subsequent conversion to β-ionone. For this task, we integrated systematically the heterologous carotenogenic genes (CrtE, CrtYB and CrtI) from Xanthophyllomyces dendrorhous using markerless genome editing CRISPR/Cas9 technology; and evaluated the transcriptional unit architecture (bidirectional or tandem), integration site, and impact of gene dosage, first on β-carotene accumulation, and later, on β-ionone production. A single-copy insertion of the carotenogenic genes in high expression loci of the wild-type yeast CEN.Pk2 strain yielded 4 mg/gDCW of total carotenoids, regardless of the transcriptional unit architecture employed. Subsequent fine-tuning of the carotenogenic gene expression enabled reaching 16 mg/gDCW of total carotenoids, which was further increased to 32 mg/gDCW by alleviating the known pathway bottleneck catalyzed by the hydroxymethylglutaryl-CoA reductase (HMGR1). The latter yield represents the highest total carotenoid concentration reported to date in S. cerevisiae for a constitutive expression system. For β-ionone synthesis, single and multiple copies of the carotene cleavage dioxygenase 1 (CCD1) gene from Petunia hybrida (PhCCD1) fused with a membrane destination peptide were expressed in the highest β-carotene-producing strains, reaching up to 33 mg/L of β-ionone in the culture medium after 72-h cultivation in shake flasks. Finally, interrogation of a contextualized genome-scale metabolic model of the producer strains pointed to PhCCD1 unspecific cleavage activity as a potentially limiting factor reducing β-ionone production. Overall, the results of this work constitute a step toward the industrial production of this ionone and, more broadly, they demonstrate that biotechnological production of apocarotenoids is technically feasible.
Collapse
Affiliation(s)
- Javiera López
- Centro de Aromas y Sabores, DICTUC S.A., Santiago, Chile
| | - Diego Bustos
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Conrado Camilo
- Centro de Aromas y Sabores, DICTUC S.A., Santiago, Chile
| | - Natalia Arenas
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pedro A Saa
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo Agosin
- Centro de Aromas y Sabores, DICTUC S.A., Santiago, Chile.,Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| |
Collapse
|
69
|
Wu Y, Liu Y, Lv X, Li J, Du G, Liu L. Applications of CRISPR in a Microbial Cell Factory: From Genome Reconstruction to Metabolic Network Reprogramming. ACS Synth Biol 2020; 9:2228-2238. [PMID: 32794766 DOI: 10.1021/acssynbio.0c00349] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The well-designed microbial cell factory finds wide applications in chemical, pharmaceutical, and food industries due to its sustainable and environmentally friendly features. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) systems have been developed into powerful tools to perform genome editing and transcriptional regulation in prokaryotic and eukaryotic cells. Accordingly, these tools are useful to build microbial cell factories not only by reconstructing the genome but also by reprogramming the metabolic network. In this review, we summarize the recent significant headway and potential uses of the CRISPR technology in the construction of efficient microbial cell factories. Moreover, the future perspectives on the improvement and upgradation of CRISPR-based tools are also discussed.
Collapse
Affiliation(s)
- Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| |
Collapse
|
70
|
Zhou K, Ng W, Cortés-Peña Y, Wang X. Increasing metabolic pathway flux by using machine learning models. Curr Opin Biotechnol 2020; 66:179-185. [PMID: 32896771 DOI: 10.1016/j.copbio.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 01/19/2023]
Abstract
Machine learning is transforming many industries through self-improving models that are fueled by big data and high computing power. The field of metabolic engineering, which uses cellular biochemical network to manufacture useful small molecules, has also witnessed the first wave of machine learning applications in the past five years, covering reaction route design, enzyme selection, pathway engineering and process optimization. This review focuses on pathway engineering, and uses a few recent studies to illustrate (1) how machine learning models can be useful in overcoming an evident rate-limiting step, and (2) how the models may be used to exhaustively search - or guide optimization algorithms to search - a large design space when the cellular regulation of the reaction network is more convoluted.
Collapse
Affiliation(s)
- Kang Zhou
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore.
| | - Wenfa Ng
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore
| | - Yoel Cortés-Peña
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore; Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Xiaonan Wang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 117585, Singapore
| |
Collapse
|
71
|
Zhao Y, Yao Z, Ploessl D, Ghosh S, Monti M, Schindler D, Gao M, Cai Y, Qiao M, Yang C, Cao M, Shao Z. Leveraging the Hermes Transposon to Accelerate the Development of Nonconventional Yeast-based Microbial Cell Factories. ACS Synth Biol 2020; 9:1736-1752. [PMID: 32396718 DOI: 10.1021/acssynbio.0c00123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We broadened the usage of DNA transposon technology by demonstrating its capacity for the rapid creation of expression libraries for long biochemical pathways, which is beyond the classical application of building genome-scale knockout libraries in yeasts. This strategy efficiently leverages the readily available fine-tuning impact provided by the diverse transcriptional environment surrounding each random integration locus. We benchmark the transposon-mediated integration against the nonhomologous end joining-mediated strategy. The latter strategy was demonstrated for achieving pathway random integration in other yeasts but is associated with a high false-positive rate in the absence of a high-throughput screening method. Our key innovation of a nonreplicable circular DNA platform increased the possibility of identifying top-producing variants to 97%. Compared to the classical DNA transposition protocol, the design of a nonreplicable circular DNA skipped the step of counter-selection for plasmid removal and thus not only reduced the time required for the step of library creation from 10 to 5 d but also efficiently removed the "transposition escapers", which undesirably represented almost 80% of the entire population as false positives. Using one endogenous product (i.e., shikimate) and one heterologous product (i.e., (S)-norcoclaurine) as examples, we presented a streamlined procedure to rapidly identify high-producing variants with titers significantly higher than the reported data in the literature. We selected Scheffersomyces stipitis, a representative nonconventional yeast, as a demo, but the strategy can be generalized to other nonconventional yeasts. This new exploration of transposon technology, therefore, adds a highly versatile tool to accelerate the development of novel species as microbial cell factories for producing value-added chemicals.
Collapse
Affiliation(s)
- Yuxin Zhao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zhanyi Yao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Saptarshi Ghosh
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Marco Monti
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Daniel Schindler
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Yizhi Cai
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, U.K
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Chao Yang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, China
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, Iowa, United States
- Bioeconomy Institute, Iowa State University, Ames, Iowa, United States
- Interdepartmental Microbiology Program, Iowa State University, Ames, Iowa, United States
- The Ames Laboratory, Ames, Iowa, United States
| |
Collapse
|
72
|
Barcelos MCS, Ramos CL, Kuddus M, Rodriguez-Couto S, Srivastava N, Ramteke PW, Mishra PK, Molina G. Enzymatic potential for the valorization of agro-industrial by-products. Biotechnol Lett 2020; 42:1799-1827. [DOI: 10.1007/s10529-020-02957-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022]
|
73
|
Liu T, Dong C, Qi M, Zhang B, Huang L, Xu Z, Lian J. Construction of a Stable and Temperature-Responsive Yeast Cell Factory for Crocetin Biosynthesis Using CRISPR-Cas9. Front Bioeng Biotechnol 2020; 8:653. [PMID: 32695754 PMCID: PMC7339864 DOI: 10.3389/fbioe.2020.00653] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/27/2020] [Indexed: 12/23/2022] Open
Abstract
Crocetin is a plant natural product with broad medicinal applications, such as improvement of sleep quality and attenuation of physical fatigue. However, crocetin production using microbial cell factories is still far from satisfaction, probably due to the conflict between cell growth and product accumulation. In the present work, a temperature-responsive crocetin-producing Saccharomyces cerevisiae strain was established to coordinate cell growth, precursor (zeaxanthin) generation, and product (crocetin) biosynthesis. The production of crocetin was further enhanced via increasing the copy numbers of CCD2 and ALDH genes using the CRISPR-Cas9 based multiplex genome integration technology. The final engineered strain TL009 produced crocetin up to 139.67 ± 2.24 μg/g DCW. The advantage of the temperature switch based crocetin production was particularly demonstrated by much higher zeaxanthin conversion yield. This study highlights the potential of the temperature-responsive yeast platform strains to increase the production of other valuable carotenoid derivatives.
Collapse
Affiliation(s)
- Tengfei Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Mingming Qi
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Bei Zhang
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.,Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| |
Collapse
|
74
|
Ding W, Zhang Y, Shi S. Development and Application of CRISPR/Cas in Microbial Biotechnology. Front Bioeng Biotechnol 2020; 8:711. [PMID: 32695770 PMCID: PMC7338305 DOI: 10.3389/fbioe.2020.00711] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/08/2020] [Indexed: 02/06/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has been rapidly developed as versatile genomic engineering tools with high efficiency, accuracy and flexibility, and has revolutionized traditional methods for applications in microbial biotechnology. Here, key points of building reliable CRISPR/Cas system for genome engineering are discussed, including the Cas protein, the guide RNA and the donor DNA. Following an overview of various CRISPR/Cas tools for genome engineering, including gene activation, gene interference, orthogonal CRISPR systems and precise single base editing, we highlighted the application of CRISPR/Cas toolbox for multiplexed engineering and high throughput screening. We then summarize recent applications of CRISPR/Cas systems in metabolic engineering toward production of chemicals and natural compounds, and end with perspectives of future advancements.
Collapse
Affiliation(s)
- Wentao Ding
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China.,Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yang Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
| |
Collapse
|
75
|
Qi DD, Jin J, Liu D, Jia B, Yuan YJ. In vitro and in vivo recombination of heterologous modules for improving biosynthesis of astaxanthin in yeast. Microb Cell Fact 2020; 19:103. [PMID: 32398013 PMCID: PMC7216642 DOI: 10.1186/s12934-020-01356-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 04/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Astaxanthin is a kind of tetraterpene and has strong antioxygenic property. The biosynthesis of astaxanthin in engineered microbial chassis has greater potential than its chemical synthesis and extraction from natural producers in an environmental-friendly way. However, the cost-offsetting production of astaxanthin in engineered microbes is still constrained by the poor efficiency of astaxanthin synthesis pathway as a heterologous pathway. RESULTS To address the bottleneck of limited production of astaxanthin in microbes, we developed in vitro and in vivo recombination methods respectively in engineered yeast chassis to optimize the combination of heterologous β-carotene ketolase (crtW) and hydroxylase (crtZ) modules that were selected from different species. As a result, the in vitro and in vivo recombination methods enhanced the astaxanthin yield respectively to 2.11-8.51 folds and 3.0-9.71 folds compared to the initial astaxanthin pathway, according to the different combination of particular genes. The highest astaxanthin producing strain yQDD022 was constructed by in vivo method and produced 6.05 mg g-1 DCW of astaxanthin. Moreover, it was proved that the in vivo recombination method showed higher DNA-assembling efficiency than the in vitro method and contributed to higher stability to the engineered yeast strains. CONCLUSIONS The in vitro and in vivo recombination methods of heterologous modules provide simple and efficient ways to improve the astaxanthin yield in yeast. Both the two methods enable high-throughput screening of heterologous pathways through recombination of certain crtW and crtZ derived from different species. This study not only exploited the underlying optimal combination of crtZ and crtW for astaxanthin synthesis, but also provided a general approach to evolve a heterologous pathway for the enhanced accumulation of desired biochemical products.
Collapse
Affiliation(s)
- Dan-Dan Qi
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Jin Jin
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Duo Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China. .,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Ying-Jin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| |
Collapse
|
76
|
Rainha J, Gomes D, Rodrigues LR, Rodrigues JL. Synthetic Biology Approaches to Engineer Saccharomyces cerevisiae towards the Industrial Production of Valuable Polyphenolic Compounds. Life (Basel) 2020; 10:life10050056. [PMID: 32370107 PMCID: PMC7281501 DOI: 10.3390/life10050056] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/22/2020] [Accepted: 04/30/2020] [Indexed: 12/27/2022] Open
Abstract
Polyphenols are plant secondary metabolites with diverse biological and potential therapeutic activities such as antioxidant, anti-inflammatory and anticancer, among others. However, their extraction from the native plants is not enough to satisfy the increasing demand for this type of compounds. The development of microbial cell factories to effectively produce polyphenols may represent the most attractive solution to overcome this limitation and produce high amounts of these bioactive molecules. With the advances in the synthetic biology field, the development of efficient microbial cell factories has become easier, largely due to the development of the molecular biology techniques and by the identification of novel isoenzymes in plants or simpler organisms to construct the heterologous pathways. Furthermore, efforts have been made to make the process more profitable through improvements in the host chassis. In this review, advances in the production of polyphenols by genetically engineered Saccharomyces cerevisiae as well as by synthetic biology and metabolic engineering approaches to improve the production of these compounds at industrial settings are discussed.
Collapse
|
77
|
Thak EJ, Yoo SJ, Moon HY, Kang HA. Yeast synthetic biology for designed cell factories producing secretory recombinant proteins. FEMS Yeast Res 2020; 20:5721243. [DOI: 10.1093/femsyr/foaa009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
ABSTRACT
Yeasts are prominent hosts for the production of recombinant proteins from industrial enzymes to therapeutic proteins. Particularly, the similarity of protein secretion pathways between these unicellular eukaryotic microorganisms and higher eukaryotic organisms has made them a preferential host to produce secretory recombinant proteins. However, there are several bottlenecks, in terms of quality and quantity, restricting their use as secretory recombinant protein production hosts. In this mini-review, we discuss recent developments in synthetic biology approaches to constructing yeast cell factories endowed with enhanced capacities of protein folding and secretion as well as designed targeted post-translational modification process functions. We focus on the new genetic tools for optimizing secretory protein expression, such as codon-optimized synthetic genes, combinatory synthetic signal peptides and copy number-controllable integration systems, and the advanced cellular engineering strategies, including endoplasmic reticulum and protein trafficking pathway engineering, synthetic glycosylation, and cell wall engineering, for improving the quality and yield of secretory recombinant proteins.
Collapse
Affiliation(s)
- Eun Jung Thak
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Su Jin Yoo
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hye Yun Moon
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| | - Hyun Ah Kang
- Laboratory of Molecular Systems Biology, Department of Life Science, Chung-Ang University, Seoul 06974, South Korea
| |
Collapse
|
78
|
A genetic toolbox for metabolic engineering of Issatchenkia orientalis. Metab Eng 2020; 59:87-97. [PMID: 32007615 DOI: 10.1016/j.ymben.2020.01.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 01/09/2020] [Accepted: 01/21/2020] [Indexed: 01/01/2023]
Abstract
The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis, which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis.
Collapse
|
79
|
Huang S, Geng A. High-copy genome integration of 2,3-butanediol biosynthesis pathway in Saccharomyces cerevisiae via in vivo DNA assembly and replicative CRISPR-Cas9 mediated delta integration. J Biotechnol 2020; 310:13-20. [PMID: 32006629 DOI: 10.1016/j.jbiotec.2020.01.014] [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: 09/18/2019] [Revised: 01/22/2020] [Accepted: 01/28/2020] [Indexed: 12/16/2022]
Abstract
CRISPR Cas9 system is becoming an emerging genome-editing platform and has been widely used for multiplex genome engineering of Saccharomyces cerevisiae. In this study, we developed a novel replicative and integrative CRISPR Cas9 genome-editing platform for large DNA construct in vivo assembly, replication, and high-copy genome integration in Saccharomyces cerevisiae. It harnessed advantages of autonomous replicative sequence in S. cerevisiae, in vivo DNA assembly, CRISPR Cas9, and delta integration. Enhanced green fluorescent protein was used as a marker to confirm large DNA construct in vivo assembly and genome integration. Based on this platform, an efficient 2,3- BDO producing yeast strain was rapidly constructed with up to 25-copy genome integration of 2,3-BDO biosynthesis pathway. Further strain engineering was conducted by multiplex disruption of ADH1, PDC1, PDC5 and MTH1 using a 2μ-based replicative CRISPR Cas9 plasmid containing donor DNAs. As a result, the 2,3-BDO titer was improved by 3.9 folds compared to that obtained by the initially engineered yeast and 50.5 g/L 2,3-BDO was produced by the final engineered yeast strain 36aS5-CFBDO in fed-batch fermentation without strain evolution and process optimization. This study demonstrated that the new replicative and integrative CRISPR Cas9 genome-editing platform was promising in generating an efficient 2,3-BDO-producing S. cerevisiae strain.
Collapse
Affiliation(s)
- Shuangcheng Huang
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore.
| | - Anli Geng
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Singapore.
| |
Collapse
|
80
|
Zhang L, Zhang H, Liu Y, Zhou J, Shen W, Liu L, Li Q, Chen X. A CRISPR-Cas9 system for multiple genome editing and pathway assembly in Candida tropicalis. Biotechnol Bioeng 2019; 117:531-542. [PMID: 31654413 DOI: 10.1002/bit.27207] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 10/09/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023]
Abstract
Genetic manipulation is among the most important tools for synthetic biology; however, modifying multiple genes is extremely time-consuming and can sometimes be impossible when dealing with gene families. Here, we present a clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein 9 (Cas9) system for use in the diploid yeast Candida tropicalis that is vastly superior to traditional techniques. This system enables the rapid and reliable introduction of multiple genetic deletions or mutations, as well as a stable expression using an integrated CRISPR-Cas9 cassette or a transient CRISPR-Cas9 cassette, together with a short donor DNA. We further show that the system can be used to promote the in vivo assembly of multiple DNA fragments and their stable integration into a target locus (or loci) in C. tropicalis. Based on this system, we present a platform for the biosynthesis of β-carotene and its derivatives. These results enable the practical application of C. tropicalis and the application of the system to other organisms.
Collapse
Affiliation(s)
- Lihua Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Haibing Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yufei Liu
- School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jingyu Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wei Shen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Liming Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xianzhong Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,School of Biotechnology, Jiangnan University, Wuxi, China
| |
Collapse
|
81
|
Deaner M, Alper HS. Enhanced scale and scope of genome engineering and regulation using CRISPR/Cas in Saccharomyces cerevisiae. FEMS Yeast Res 2019; 19:foz076. [PMID: 31665284 DOI: 10.1093/femsyr/foz076] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 10/24/2019] [Indexed: 12/13/2022] Open
Abstract
Although only 6 years old, the CRISPR system has blossomed into a tool for rapid, on-demand genome engineering and gene regulation in Saccharomyces cerevisiae. In this minireview, we discuss fundamental CRISPR technologies, tools to improve the efficiency and capabilities of gene targeting, and cutting-edge techniques to explore gene editing and transcriptional regulation at genome scale using pooled approaches. The focus is on applications to metabolic engineering with topics including development of techniques to edit the genome in multiplex, tools to enable large numbers of genetic modifications using pooled single-guide RNA libraries and efforts to enable programmable transcriptional regulation using endonuclease-null Cas enzymes.
Collapse
Affiliation(s)
- Matthew Deaner
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, USA
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, USA
| |
Collapse
|
82
|
Zhang C, Xue Q, Hou J, Mohsin A, Zhang M, Guo M, Zhu Y, Bao J, Wang J, Xiao W, Cao L. In-Depth Two-Stage Transcriptional Reprogramming and Evolutionary Engineering of Saccharomyces cerevisiae for Efficient Bioethanol Production from Xylose with Acetate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:12002-12012. [PMID: 31595746 DOI: 10.1021/acs.jafc.9b05095] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In order to achieve rapid xylose utilization in the presence of acetate, improved yeast strains were engineered for higher bioethanol production. First, a six-gene cluster, including XYL1/XYL2/XKS1/TAL1/PYK1/MGT05196, was generated by using an in-depth two-stage (glucose and xylose) transcription reprogramming strategy in an evolutionary adapted strain of CE7, resulting in two improved engineered strains WXY46 and WXY53. Through a combined screening of xylose and glucose stage-specific promoters between tricarboxylic acid (TCA)/HSP and constitutive types, respectively, WXY46 with the constitutive promoters showed a much higher ethanol yield than that of WXY53 with the TCA/HSP promoters. Second, an optimized strain WXY74 was obtained by using more copies of a six-gene cluster, which resulted in a higher ethanol yield of 0.500 g/g total sugars with acetate conditions. At last, simultaneous saccharification and co-fermentation were performed by using the evolved WXY74 strain, which produced 58.4 g/L of ethanol from wheat straw waste and outperformed previous haploid XR-XDH strains.
Collapse
Affiliation(s)
- Cheng Zhang
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Qian Xue
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Junyan Hou
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Ali Mohsin
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Mei Zhang
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Meijin Guo
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Yixuan Zhu
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Jingyu Wang
- Department of Chemical Engineering and Materials Science , University of Minnesota , Twin Cities, Minneapolis , Minnesota 55455 , United States
| | - Wei Xiao
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| | - Limin Cao
- College of Life Sciences , Capital Normal University , Beijing 100048 , China
| |
Collapse
|
83
|
CRISPR/Transposon gene integration (CRITGI) can manage gene expression in a retrotransposon-dependent manner. Sci Rep 2019; 9:15300. [PMID: 31653950 PMCID: PMC6814769 DOI: 10.1038/s41598-019-51891-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/09/2019] [Indexed: 12/04/2022] Open
Abstract
The fine-tuning of gene expression contributes to both basic science and applications. Here, we develop a novel gene expression technology termed CRITGI (CRISPR/Transposon gene integration). CRITGI uses CRISPR/Cas9 to integrate multiple copies of the plasmid pTy1 into Ty1 loci, budding yeast retrotransposons. The pTy1 plasmid harbors a Ty1 consensus sequence for integration, a gene of interest with its own promoter and a selection marker gene. Interestingly, the expression of the pTy1 gene in Ty1 loci could be induced in synthetic complete amino acid depletion medium, which could activate the selection marker gene on pTy1. The induction or repression of the gene on pTy1 depended on Ty1 transcription. Activation of the selection marker gene on pTy1 triggered Ty1 transcription, which led to induction of the gene on pTy1. The gene on pTy1 was not transcribed with Ty1 mRNA; the transcription required its own promoter. Furthermore, the trimethylation of histone H3 on lysine 4, a landmark of transcriptionally active chromatin, accumulated at the 5′ end of the gene on pTy1 following selection marker gene activation. Thus, CRITGI is a unique gene regulation system to induce the genes on pTy1 in amino acid depletion medium and utilizes Ty1 transcription to create a chromatin environment favorable for the transcription of the genes on pTy1.
Collapse
|
84
|
Yadav M, Shukla P. Efficient engineered probiotics using synthetic biology approaches: A review. Biotechnol Appl Biochem 2019; 67:22-29. [PMID: 31538358 DOI: 10.1002/bab.1822] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/13/2019] [Indexed: 12/14/2022]
Abstract
The uses of probiotics-based food supplements are getting emphasis due to their power to ensure better health conditions. Probiotics have diverse and significant applications in the health sector, so probiotic strains require an understanding of the genome level organizations. Probiotics elucidate various functional parameters that control their metabolic functions. In this review, we have compiled aspects of synthetic biology, which are used for the optimization of metabolic processes in probiotics for their use as a supplement in allopathic medicines. Synthetic biology approaches provide information about diverse biosynthetic pathways and also facilitate the novel metabolic engineering approaches for probiotics strain improvement. We have discussed the synthetic biology approaches for producing engineered probiotics via genetic circuits, expression systems, and genome editing tools like CRISPR-Cas and PEVLAB. This review also enlightens future challenges in the development of engineered probiotics.
Collapse
Affiliation(s)
- Monika Yadav
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India
| |
Collapse
|
85
|
Yee DA, DeNicola AB, Billingsley JM, Creso JG, Subrahmanyam V, Tang Y. Engineered mitochondrial production of monoterpenes in Saccharomyces cerevisiae. Metab Eng 2019; 55:76-84. [PMID: 31226348 PMCID: PMC6717016 DOI: 10.1016/j.ymben.2019.06.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022]
Abstract
Monoterpene indole alkaloids (MIAs) from plants encompass a broad class of structurally complex and medicinally valuable natural products. MIAs are biologically derived from the universal precursor strictosidine. Although the strictosidine biosynthetic pathway has been identified and reconstituted, extensive work is required to optimize production of strictosidine and its precursors in yeast. In this study, we engineered a fully integrated and plasmid-free yeast strain with enhanced production of the monoterpene precursor geraniol. The geraniol biosynthetic pathway was targeted to the mitochondria to protect the GPP pool from consumption by the cytosolic ergosterol pathway. The mitochondrial geraniol producer showed a 6-fold increase in geraniol production compared to cytosolic producing strains. We further engineered the monoterpene-producing strain to synthesize the next intermediates in the strictosidine pathway: 8-hydroxygeraniol and nepetalactol. Integration of geraniol hydroxylase (G8H) from Catharanthus roseus led to essentially quantitative conversion of geraniol to 8-hydroxygeraniol at a titer of 227 mg/L in a fed-batch fermentation. Further introduction of geraniol oxidoreductase (GOR) and iridoid synthase (ISY) from C. roseus and tuning of the relative expression levels resulted in the first de novo nepetalactol production. The strategies developed in this work can facilitate future strain engineering for yeast production of later intermediates in the strictosidine biosynthetic pathway.
Collapse
Affiliation(s)
- Danielle A Yee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, United States
| | - Anthony B DeNicola
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, United States
| | - John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, United States
| | - Jenette G Creso
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, United States
| | - Vidya Subrahmanyam
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, 90095, United States; Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, United States.
| |
Collapse
|
86
|
Nora LC, Westmann CA, Guazzaroni ME, Siddaiah C, Gupta VK, Silva-Rocha R. Recent advances in plasmid-based tools for establishing novel microbial chassis. Biotechnol Adv 2019; 37:107433. [PMID: 31437573 DOI: 10.1016/j.biotechadv.2019.107433] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 07/11/2019] [Accepted: 08/16/2019] [Indexed: 12/28/2022]
Abstract
A key challenge for domesticating alternative cultivable microorganisms with biotechnological potential lies in the development of innovative technologies. Within this framework, a myriad of genetic tools has flourished, allowing the design and manipulation of complex synthetic circuits and genomes to become the general rule in many laboratories rather than the exception. More recently, with the development of novel technologies such as DNA automated synthesis/sequencing and powerful computational tools, molecular biology has entered the synthetic biology era. In the beginning, most of these technologies were established in traditional microbial models (known as chassis in the synthetic biology framework) such as Escherichia coli and Saccharomyces cerevisiae, enabling fast advances in the field and the validation of fundamental proofs of concept. However, it soon became clear that these organisms, although extremely useful for prototyping many genetic tools, were not ideal for a wide range of biotechnological tasks due to intrinsic limitations in their molecular/physiological properties. Over the last decade, researchers have been facing the great challenge of shifting from these model systems to non-conventional chassis with endogenous capacities for dealing with specific tasks. The key to address these issues includes the generation of narrow and broad host plasmid-based molecular tools and the development of novel methods for engineering genomes through homologous recombination systems, CRISPR/Cas9 and other alternative methods. Here, we address the most recent advances in plasmid-based tools for the construction of novel cell factories, including a guide for helping with "build-your-own" microbial host.
Collapse
Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - María-Eugenia Guazzaroni
- Faculty of Philosophy, Science and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | | | - Vijai Kumar Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Rafael Silva-Rocha
- Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil.
| |
Collapse
|
87
|
Dong H, Zheng J, Yu D, Wang B, Pan L. Efficient genome editing in Aspergillus niger with an improved recyclable CRISPR-HDR toolbox and its application in introducing multiple copies of heterologous genes. J Microbiol Methods 2019; 163:105655. [DOI: 10.1016/j.mimet.2019.105655] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/13/2019] [Accepted: 06/13/2019] [Indexed: 11/25/2022]
|
88
|
CRISPR system in the yeast Saccharomyces cerevisiae and its application in the bioproduction of useful chemicals. World J Microbiol Biotechnol 2019; 35:111. [DOI: 10.1007/s11274-019-2688-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 06/30/2019] [Indexed: 12/16/2022]
|
89
|
Song X, Li Y, Wu Y, Cai M, Liu Q, Gao K, Zhang X, Bai Y, Xu H, Qiao M. Metabolic engineering strategies for improvement of ethanol production in cellulolytic Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:5071949. [PMID: 30107496 DOI: 10.1093/femsyr/foy090] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/09/2018] [Indexed: 01/31/2023] Open
Abstract
As a traditional ethanol-producing microorganism, Saccharomyces cerevisiae is an ideal host for consolidated bioprocessing. However, expression of heterologous cellulase increases the metabolic burden in yeast, which results in low cellulase activity and poor cellulose degradation efficiency. In this study, cellulase-expressing yeast strains that could efficiently degrade different cellulosic substrates were created by optimizing cellulase ratios through a POT1-mediated δ-integration strategy. Metabolic engineering strategies, including optimization of codon usage, promoter and signal peptide, were also included in this system. We also confirmed that heterologous cellulase expression in cellulosic yeast induced the unfolded protein response. To enhance protein folding capacity, the endoplasmic reticulum chaperone protein BiP and the disulfide isomerase Pdi1p were overexpressed, and the Golgi membrane protein Ca2+/Mn2+ ATPase Pmr1p was disrupted to decrease the glycosylation of cellulase. The resultant strain, SK18-3, could produce 5.4 g L-1 ethanol with carboxymethyl-cellulose. Strain SK12-50 achieved 4.7 g L-1 ethanol production with phosphoric acid swollen cellulose hydrolysis. When Avicel was used as the substrate, 3.8 g L-1 ethanol (75% of the theoretical maximum yield) was produced in SK13-34. This work will significantly increase our knowledge of how to engineer optimal yeast strains for biofuel production from cellulosic biomass.
Collapse
Affiliation(s)
- Xiaofei Song
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Yuanzi Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Yuzhen Wu
- Department of Microbiology, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Miao Cai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Quanli Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Kai Gao
- Tianjin Academy of Environmental Sciences, No. 17 Fukang Road, Nankai District, Tianjin 300071, China
| | - Xiuming Zhang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Yanling Bai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Haijin Xu
- Department of Microbiology, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| |
Collapse
|
90
|
Li L, Liu X, Wei K, Lu Y, Jiang W. Synthetic biology approaches for chromosomal integration of genes and pathways in industrial microbial systems. Biotechnol Adv 2019; 37:730-745. [PMID: 30951810 DOI: 10.1016/j.biotechadv.2019.04.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
Industrial biotechnology is reliant on native pathway engineering or foreign pathway introduction for efficient biosynthesis of target products. Chromosomal integration, with intrinsic genetic stability, is an indispensable step for reliable expression of homologous or heterologous genes and pathways in large-scale and long-term fermentation. With advances in synthetic biology and CRISPR-based genome editing approaches, a wide variety of novel enabling technologies have been developed for single-step, markerless, multi-locus genomic integration of large biochemical pathways, which significantly facilitate microbial overproduction of chemicals, pharmaceuticals and other value-added biomolecules. Notably, the newly discovered homology-mediated end joining strategy could be widely applicable for high-efficiency genomic integration in a number of homologous recombination-deficient microbes. In this review, we explore the fundamental principles and characteristics of genomic integration, and highlight the development and applications of targeted integration approaches in the three representative industrial microbial systems, including Escherichia coli, actinomycetes and yeasts.
Collapse
Affiliation(s)
- Lei Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Xiaocao Liu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Keke Wei
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, 200232, China.
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.
| |
Collapse
|
91
|
Adames NR, Gallegos JE, Peccoud J. Yeast genetic interaction screens in the age of CRISPR/Cas. Curr Genet 2019; 65:307-327. [PMID: 30255296 PMCID: PMC6420903 DOI: 10.1007/s00294-018-0887-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/14/2018] [Accepted: 09/18/2018] [Indexed: 12/21/2022]
Abstract
The ease of performing both forward and reverse genetics in Saccharomyces cerevisiae, along with its stable haploid state and short generation times, has made this budding yeast the consummate model eukaryote for genetics. The major advantage of using budding yeast for reverse genetics is this organism's highly efficient homology-directed repair, allowing for precise genome editing simply by introducing DNA with homology to the chromosomal target. Although plasmid- and PCR-based genome editing tools are quite efficient, they depend on rare spontaneous DNA breaks near the target sequence. Consequently, they can generate only one genomic edit at a time, and the edit must be associated with a selectable marker. However, CRISPR/Cas technology is efficient enough to permit markerless and multiplexed edits in a single step. These features have made CRISPR/Cas popular for yeast strain engineering in synthetic biology and metabolic engineering applications, but it has not been widely employed for genetic screens. In this review, we critically examine different methods to generate multi-mutant strains in systematic genetic interaction screens and discuss the potential of CRISPR/Cas to supplement or improve on these methods.
Collapse
Affiliation(s)
- Neil R Adames
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jenna E Gallegos
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jean Peccoud
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, 80523, USA.
| |
Collapse
|
92
|
Abstract
With the rapid development of DNA synthesis and next-generation sequencing, synthetic biology that aims to standardize, modularize, and innovate cellular functions, has achieved vast progress. Here we review key advances in synthetic biology of the yeast Saccharomyces cerevisiae, which serves as an important eukaryal model organism and widely applied cell factory. This covers the development of new building blocks, i.e., promoters, terminators and enzymes, pathway engineering, tools developments, and gene circuits utilization. We will also summarize impacts of synthetic biology on both basic and applied biology, and end with further directions for advancing synthetic biology in yeast.
Collapse
Affiliation(s)
- Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing Key Laboratory of Bioprocess , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yueping Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing Key Laboratory of Bioprocess , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing Key Laboratory of Bioprocess , Beijing University of Chemical Technology , Beijing 100029 , China.,Department of Biology and Biological Engineering , Chalmers University of Technology , Gothenburg SE41296 , Sweden.,Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , Kongens Lyngby DK2800 , Denmark
| |
Collapse
|
93
|
Shi S, Liang Y, Ang EL, Zhao H. Delta Integration CRISPR-Cas (Di-CRISPR) in Saccharomyces cerevisiae. Methods Mol Biol 2019; 1927:73-91. [PMID: 30788786 DOI: 10.1007/978-1-4939-9142-6_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Despite the advances made in genetic engineering of Saccharomyces cerevisiae, the multicopy genomic integration of large biochemical pathways remains a challenge. Here, we developed a Di-CRISPR (delta integration CRISPR-Cas) platform based on cleavage of the delta sites by Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated systems (Cas) to enable unprecedented high-efficiency, multicopy, markerless integrations of large biochemical pathways into the S. cerevisiae genome. Detailed protocols are provided on the entire workflow which includes pDi-CRISPR plasmid and donor DNA construction, Di-CRISPR-mediated integration and analysis of integration efficiencies and copy numbers through flow cytometry and quantitative polymerase chain reaction (qPCR).
Collapse
Affiliation(s)
- Shuobo Shi
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore
| | - Youyun Liang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore, Singapore.
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
94
|
Nora LC, Westmann CA, Martins‐Santana L, Alves LDF, Monteiro LMO, Guazzaroni M, Silva‐Rocha R. The art of vector engineering: towards the construction of next-generation genetic tools. Microb Biotechnol 2019; 12:125-147. [PMID: 30259693 PMCID: PMC6302727 DOI: 10.1111/1751-7915.13318] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/29/2018] [Accepted: 08/31/2018] [Indexed: 12/20/2022] Open
Abstract
When recombinant DNA technology was developed more than 40 years ago, no one could have imagined the impact it would have on both society and the scientific community. In the field of genetic engineering, the most important tool developed was the plasmid vector. This technology has been continuously expanding and undergoing adaptations. Here, we provide a detailed view following the evolution of vectors built throughout the years destined to study microorganisms and their peculiarities, including those whose genomes can only be revealed through metagenomics. We remark how synthetic biology became a turning point in designing these genetic tools to create meaningful innovations. We have placed special focus on the tools for engineering bacteria and fungi (both yeast and filamentous fungi) and those available to construct metagenomic libraries. Based on this overview, future goals would include the development of modular vectors bearing standardized parts and orthogonally designed circuits, a task not fully addressed thus far. Finally, we present some challenges that should be overcome to enable the next generation of vector design and ways to address it.
Collapse
Affiliation(s)
- Luísa Czamanski Nora
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Cauã Antunes Westmann
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - Luana de Fátima Alves
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | | | - María‐Eugenia Guazzaroni
- School of Philosophy, Science and Letters of Ribeirão PretoUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| | - Rafael Silva‐Rocha
- Ribeirão Preto Medical SchoolUniversity of São PauloRibeirão Preto, São Paulo14049‐900Brazil
| |
Collapse
|
95
|
Liu G, Qu Y. Engineering of filamentous fungi for efficient conversion of lignocellulose: Tools, recent advances and prospects. Biotechnol Adv 2018; 37:519-529. [PMID: 30576717 DOI: 10.1016/j.biotechadv.2018.12.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 01/17/2023]
Abstract
Filamentous fungi, as the main producers of lignocellulolytic enzymes in industry, need to be engineered to improve the economy of large-scale lignocellulose conversion. Investigation of the cellular processes involved in lignocellulolytic enzyme production, as well as optimization of enzyme mixtures for higher hydrolysis efficiency, have provided effective targets for the engineering of lignocellulolytic fungi. Recently, the development of efficient genetic manipulation systems in several lignocellulolytic fungi opens up the possibility of systems engineering of these strains. Here, we review the recent progresses made in the engineering of lignocellulolytic fungi and highlight the research gaps in this area.
Collapse
Affiliation(s)
- Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China
| | - Yinbo Qu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; National Glycoengineering Research Center, Shandong University, Qingdao 266237, China.
| |
Collapse
|
96
|
Cui Z, Jiang X, Zheng H, Qi Q, Hou J. Homology‐independent genome integration enables rapid library construction for enzyme expression and pathway optimization inYarrowia lipolytica. Biotechnol Bioeng 2018; 116:354-363. [DOI: 10.1002/bit.26863] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/02/2018] [Accepted: 11/07/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
| | - Xin Jiang
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
| | - Huihui Zheng
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
- CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of SciencesQingdao China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong UniversityQingdao China
| |
Collapse
|
97
|
Li L, Wei K, Liu X, Wu Y, Zheng G, Chen S, Jiang W, Lu Y. aMSGE: advanced multiplex site-specific genome engineering with orthogonal modular recombinases in actinomycetes. Metab Eng 2018; 52:153-167. [PMID: 30529239 DOI: 10.1016/j.ymben.2018.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 11/18/2022]
Abstract
Chromosomal integration of genes and pathways is of particular importance for large-scale and long-term fermentation in industrial biotechnology. However, stable, multi-copy integration of long DNA segments (e.g., large gene clusters) remains challenging. Here, we describe a plug-and-play toolkit that allows for high-efficiency, single-step, multi-locus integration of natural product (NP) biosynthetic gene clusters (BGCs) in actinomycetes, based on the innovative concept of "multiple integrases-multiple attB sites". This toolkit consists of 27 synthetic modular plasmids, which contain single- or multi-integration modules (from two to four) derived from five orthogonal site-specific recombination (SSR) systems. The multi-integration modules can be readily ligated into plasmids containing large BGCs by Gibson assembly, which can be simultaneously inserted into multiple native attB sites in a single step. We demonstrated the applicability of this toolkit by performing stabilized amplification of acetyl-CoA carboxylase genes to facilitate actinorhodin biosynthesis in Streptomyces coelicolor. Furthermore, using this toolkit, we achieved a 185.6% increase in 5-oxomilbemycin titers (from 2.23 to 6.37 g/L) in Streptomyces hygroscopicus via the multi-locus integration of the entire 5-oxomilbemycin BGC (72 kb) (up to four copies). Compared with previously reported methods, the advanced multiplex site-specific genome engineering (aMSGE) method does not require the introduction of any modifications into host genomes before the amplification of target genes or BGCs, which will drastically simplify and accelerate efforts to improve NP production. Considering that SSR systems are widely distributed in a variety of industrial microbes, this novel technique also promises to be a valuable tool for the enhanced biosynthesis of other high-value bioproducts.
Collapse
Affiliation(s)
- Lei Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Keke Wei
- School of Pharmacy, Fudan University, Shanghai 201203, China; Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Xiaocao Liu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; School of Life Science, Henan University, Kaifeng 475004, China
| | - Yuanjie Wu
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Guosong Zheng
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shaoxin Chen
- Department of Biochemistry, Shanghai Institute of Pharmaceutical Industry, Shanghai 201210, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; Jiangsu National Synergetic Innovation Center for Advanced Materials, SICAM, Nanjing 210009, China.
| | - Yinhua Lu
- College of Life Sciences, Shanghai Normal University, Shanghai 200232, China.
| |
Collapse
|
98
|
Selectable marker recycling in the nonconventional yeast Xanthophyllomyces dendrorhous by transient expression of Cre on a genetically unstable vector. Appl Microbiol Biotechnol 2018; 103:963-971. [DOI: 10.1007/s00253-018-9496-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
|
99
|
Abstract
Synthetic biology has undergone dramatic advancements for over a decade, during which it has expanded our understanding on the systems of life and opened new avenues for microbial engineering. Many biotechnological and computational methods have been developed for the construction of synthetic systems. Achievements in synthetic biology have been widely adopted in metabolic engineering, a field aimed at engineering micro-organisms to produce substances of interest. However, the engineering of metabolic systems requires dynamic redistribution of cellular resources, the creation of novel metabolic pathways, and optimal regulation of the pathways to achieve higher production titers. Thus, the design principles and tools developed in synthetic biology have been employed to create novel and flexible metabolic pathways and to optimize metabolic fluxes to increase the cells’ capability to act as production factories. In this review, we introduce synthetic biology tools and their applications to microbial cell factory constructions.
Collapse
|
100
|
Bourgeois L, Pyne ME, Martin VJJ. A Highly Characterized Synthetic Landing Pad System for Precise Multicopy Gene Integration in Yeast. ACS Synth Biol 2018; 7:2675-2685. [PMID: 30372609 DOI: 10.1021/acssynbio.8b00339] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A fundamental undertaking of metabolic engineering involves identifying and troubleshooting metabolic bottlenecks that arise from imbalances in pathway flux. To expedite the systematic screening of enzyme orthologs in conjunction with DNA copy number tuning, here we develop a simple and highly characterized CRISPR-Cas9 integration system in Saccharomyces cerevisiae. Our engineering strategy introduces a series of synthetic DNA landing pads (LP) into the S. cerevisiae genome to act as sites for high-level gene integration. LPs facilitate multicopy gene integration of one, two, three, or four DNA copies in a single transformation, thus providing precise control of DNA copy number. We applied our LP system to norcoclaurine synthase (NCS), an enzyme with poor kinetic properties involved in the first committed step of the production of high-value benzylisoquinoline alkaloids. The platform enabled rapid construction of a 40-strain NCS library by integrating ten NCS orthologs in four gene copies each. Six active NCS variants were identified, whereby production of ( S)-norcoclaurine could be further enhanced by increasing NCS copy number. We anticipate the LP system will aid in metabolic engineering efforts by providing strict control of gene copy number and expediting strain and pathway engineering campaigns.
Collapse
Affiliation(s)
- Leanne Bourgeois
- Department of Biology, Concordia University, Montréal, Québec H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H3G 1M8, Canada
| | - Michael E. Pyne
- Department of Biology, Concordia University, Montréal, Québec H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H3G 1M8, Canada
| | - Vincent J. J. Martin
- Department of Biology, Concordia University, Montréal, Québec H3G 1M8, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H3G 1M8, Canada
| |
Collapse
|