1
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Liang Y, Gao S, Qi X, Valentovich LN, An Y. Progress in Gene Editing and Metabolic Regulation of Saccharomyces cerevisiae with CRISPR/Cas9 Tools. ACS Synth Biol 2024; 13:428-448. [PMID: 38326929 DOI: 10.1021/acssynbio.3c00685] [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: 02/09/2024]
Abstract
The CRISPR/Cas9 systems have been developed as tools for genetic engineering and metabolic engineering in various organisms. In this review, various aspects of CRISPR/Cas9 in Saccharomyces cerevisiae, from basic principles to practical applications, have been summarized. First, a comprehensive review has been conducted on the history of CRISPR/Cas9, successful cases of gene disruptions, and efficiencies of multiple DNA fragment insertions. Such advanced systems have accelerated the development of microbial engineering by reducing time and labor, and have enhanced the understanding of molecular genetics. Furthermore, the research progress of the CRISPR/Cas9-based systems in the production of high-value-added chemicals and the improvement of stress tolerance in S. cerevisiae have been summarized, which should have an important reference value for genetic and synthetic biology studies based on S. cerevisiae.
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Affiliation(s)
- Yaokun Liang
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Xianghui Qi
- School of Life Sciences, Guangzhou University, Guangdong 511370, China
| | - Leonid N Valentovich
- Institute of Microbiology, National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - Yingfeng An
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
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2
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Yu L, Marchisio MA. Scaffold RNA engineering in type V CRISPR-Cas systems: a potent way to enhance gene expression in the yeast Saccharomyces cerevisiae. Nucleic Acids Res 2024; 52:1483-1497. [PMID: 38142459 PMCID: PMC10853767 DOI: 10.1093/nar/gkad1216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/30/2023] [Accepted: 12/14/2023] [Indexed: 12/26/2023] Open
Abstract
New, orthogonal transcription factors in eukaryotic cells have been realized by engineering nuclease-deficient CRISPR-associated proteins and/or their guide RNAs. In this work, we present a new kind of orthogonal transcriptional activators, in Saccharomyces cerevisiae, made by turning type V CRISPR RNA into a scaffold RNA (ScRNA) able to recruit a variable number of VP64 activation domains. The activator arises from the complex between the synthetic ScRNA and DNase-deficient type V Cas proteins: dCas12e and denAsCas12a. The transcription activation achieved via the newly engineered dCas:ScRNA system is up to 4.7-fold higher than that obtained with the direct fusion of VP64 to Cas proteins. The new transcription factors have been proven to be functional in circuits such as Boolean gates, converters, multiplex-gene and metabolic-pathway activation. Our results extend the CRISPR-Cas-based technology with a new effective tool that only demands RNA engineering and improves the current design of transcription factors based on type V Cas proteins.
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Affiliation(s)
- Lifang Yu
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
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3
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Babaei M, Thomsen PT, Pastor MC, Jensen MK, Borodina I. Coupling High-Throughput and Targeted Screening for Identification of Nonobvious Metabolic Engineering Targets. ACS Synth Biol 2024; 13:168-182. [PMID: 38141039 PMCID: PMC10804409 DOI: 10.1021/acssynbio.3c00396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Identification of metabolic engineering targets is a fundamental challenge in strain development programs. While high-throughput (HTP) genetic engineering methodologies capable of generating vast diversity are being developed at a rapid rate, a majority of industrially interesting molecules cannot be screened at sufficient throughput to leverage these techniques. We propose a workflow that couples HTP screening of common precursors (e.g., amino acids) that can be screened either directly or by artificial biosensors, with low-throughput targeted validation of the molecule of interest to uncover nonintuitive beneficial metabolic engineering targets and combinations hereof. Using this workflow, we identified several nonobvious novel targets for improving p-coumaric acid (p-CA) and l-DOPA production from two large 4k gRNA libraries each deregulating 1000 metabolic genes in the yeast Saccharomyces cerevisiae. We initially screened yeast cells transformed with gRNA library plasmids for individual regulatory targets improving the production of l-tyrosine-derived betaxanthins, identifying 30 targets that increased intracellular betaxanthin content 3.5-5.7 fold. Hereafter, we screened the targets individually in a high-producing p-CA strain, narrowing down the targets to six that increased the secreted titer by up to 15%. To investigate whether any of the six targets could be additively combined to improve p-CA production further, we created a gRNA multiplexing library and subjected it to our proposed coupled workflow. The combination of regulating PYC1 and NTH2 simultaneously resulted in the highest (threefold) improvement of the betaxanthin content, and an additive trend was also observed in the p-CA strain. Lastly, we tested the initial 30 targets in a l-DOPA producing strain, identifying 10 targets that increased the secreted titer by up to 89%, further validating our screening by proxy workflow. This coupled approach is useful for strain development in the absence of direct HTP screening assays for products of interest.
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Affiliation(s)
- Mahsa Babaei
- Novo Nordisk Foundation
Center
for Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Philip Tinggaard Thomsen
- Novo Nordisk Foundation
Center
for Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Marc Cernuda Pastor
- Novo Nordisk Foundation
Center
for Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Michael Krogh Jensen
- Novo Nordisk Foundation
Center
for Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Irina Borodina
- Novo Nordisk Foundation
Center
for Biosustainability, Technical University
of Denmark, 2800 Kgs. Lyngby, Denmark
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4
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Lv X, Li Y, Xiu X, Liao C, Xu Y, Liu Y, Li J, Du G, Liu L. CRISPR genetic toolkits of classical food microorganisms: Current state and future prospects. Biotechnol Adv 2023; 69:108261. [PMID: 37741424 DOI: 10.1016/j.biotechadv.2023.108261] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 09/25/2023]
Abstract
Production of food-related products using microorganisms in an environmentally friendly manner is a crucial solution to global food safety and environmental pollution issues. Traditional microbial modification methods rely on artificial selection or natural mutations, which require time for repeated screening and reproduction, leading to unstable results. Therefore, it is imperative to develop rapid, efficient, and precise microbial modification technologies. This review summarizes recent advances in the construction of gene editing and metabolic regulation toolkits based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (CRISPR-Cas) systems and their applications in reconstructing food microorganism metabolic networks. The development and application of gene editing toolkits from single-site gene editing to multi-site and genome-scale gene editing was also introduced. Moreover, it presented a detailed introduction to CRISPR interference, CRISPR activation, and logic circuit toolkits for metabolic network regulation. Moreover, the current challenges and future prospects for developing CRISPR genetic toolkits were also discussed.
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Affiliation(s)
- 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
| | - Yang 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
| | - Xiang Xiu
- 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
| | - Chao Liao
- 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
| | - Yameng Xu
- 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
| | - 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
- 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
| | - 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; Food Laboratory of Zhongyuan, Jiangnan University, Wuxi 214122, China.
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5
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Auradkar A, Guichard A, Kaduwal S, Sneider M, Bier E. tgCRISPRi: efficient gene knock-down using truncated gRNAs and catalytically active Cas9. Nat Commun 2023; 14:5587. [PMID: 37696787 PMCID: PMC10495392 DOI: 10.1038/s41467-023-40836-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/14/2023] [Indexed: 09/13/2023] Open
Abstract
CRISPR-interference (CRISPRi), a highly effective method for silencing genes in mammalian cells, employs an enzymatically dead form of Cas9 (dCas9) complexed with one or more guide RNAs (gRNAs) with 20 nucleotides (nt) of complementarity to transcription initiation sites of target genes. Such gRNA/dCas9 complexes bind to DNA, impeding transcription of the targeted locus. Here, we present an alternative gene-suppression strategy using active Cas9 complexed with truncated gRNAs (tgRNAs). Cas9/tgRNA complexes bind to specific target sites without triggering DNA cleavage. When targeted near transcriptional start sites, these short 14-15 nts tgRNAs efficiently repress expression of several target genes throughout somatic tissues in Drosophila melanogaster without generating any detectable target site mutations. tgRNAs also can activate target gene expression when complexed with a Cas9-VPR fusion protein or modulate enhancer activity, and can be incorporated into a gene-drive, wherein a traditional gRNA sustains drive while a tgRNA inhibits target gene expression.
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Affiliation(s)
- Ankush Auradkar
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Annabel Guichard
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Saluja Kaduwal
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Marketta Sneider
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA
| | - Ethan Bier
- Department of Cell and Developmental Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0335, USA.
- Tata Institute for Genetics and Society - UCSD, La Jolla, USA.
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6
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Pham A, Bassett S, Chen W, Da Silva NA. Assembly of Metabolons in Yeast Using Cas6-Mediated RNA Scaffolding. ACS Synth Biol 2023; 12:1164-1174. [PMID: 36920425 DOI: 10.1021/acssynbio.2c00650] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Cells often localize pathway enzymes in close proximity to reduce substrate loss via diffusion and to ensure that carbon flux is directed toward the desired product. To emulate this strategy for the biosynthesis of heterologous products in yeast, we have taken advantage of the highly specific Cas6-RNA interaction and the predictability of RNA hybridizations to demonstrate Cas6-mediated RNA-guided protein assembly within the yeast cytosol. The feasibility of this synthetic scaffolding technique for protein localization was first demonstrated using a split luciferase reporter system with each part fused to a different Cas6 protein. In Saccharomyces cerevisiae, the luminescence signal increased 3.6- to 20-fold when the functional RNA scaffold was also expressed. Expression of a trigger RNA, designed to prevent the formation of a functional scaffold by strand displacement, decreased the luminescence signal by nearly 2.3-fold. Temporal control was also possible, with induction of scaffold expression resulting in an up to 11.6-fold increase in luminescence after 23 h. Cas6-mediated assembly was applied to create a two-enzyme metabolon to redirect a branch of the violacein biosynthesis pathway. Localizing VioC and VioE together increased the amount of deoxyviolacein (desired) relative to prodeoxyviolacein (undesired) by 2-fold. To assess the generality of this colocalization method in other yeast systems, the split luciferase reporter system was evaluated in Kluyveromyces marxianus; RNA scaffold expression resulted in an increase in the luminescence signal of up to 1.9-fold. The simplicity and flexibility of the design suggest that this strategy can be used to create metabolons in a wide range of recombinant hosts of interest.
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Affiliation(s)
- Anhuy Pham
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697-2580, United States
| | - Shane Bassett
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697-2580, United States
| | - Wilfred Chen
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Nancy A Da Silva
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, California 92697-2580, United States
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7
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Wu Y, Li Y, Jin K, Zhang L, Li J, Liu Y, Du G, Lv X, Chen J, Ledesma-Amaro R, Liu L. CRISPR-dCas12a-mediated genetic circuit cascades for multiplexed pathway optimization. Nat Chem Biol 2023; 19:367-377. [PMID: 36646959 DOI: 10.1038/s41589-022-01230-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/22/2022] [Indexed: 01/17/2023]
Abstract
The production efficiency of microbial cell factories is sometimes limited by the lack of effective methods to regulate multiple targets in a coordinated manner. Here taking the biosynthesis of glucosamine-6-phosphate (GlcN6P) in Bacillus subtilis as an example, a 'design-build-test-learn' framework was proposed to achieve efficient multiplexed optimization of metabolic pathways. A platform strain was built to carry biosensor signal-amplifying circuits and two genetic regulation circuits. Then, a synthetic CRISPR RNA array blend for boosting and leading (ScrABBLE) device was integrated into the platform strain, which generated 5,184 combinatorial assemblies targeting three genes. The best GlcN6P producer was screened and engineered for the synthesis of valuable pharmaceuticals N-acetylglucosamine and N-acetylmannosamine. The N-acetylglucosamine titer reached 183.9 g liter-1 in a 15-liter bioreactor. In addition, the potential generic application of the ScrABBLE device was also verified using three fluorescent proteins as a case study.
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Affiliation(s)
- Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Yang Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Linpei Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Centre for Synthetic Biology, Imperial College London, London, UK
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, China.
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8
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Ting TY, Li Y, Bunawan H, Ramzi AB, Goh HH. Current advancements in systems and synthetic biology studies of Saccharomyces cerevisiae. J Biosci Bioeng 2023; 135:259-265. [PMID: 36803862 DOI: 10.1016/j.jbiosc.2023.01.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/03/2023] [Accepted: 01/26/2023] [Indexed: 02/18/2023]
Abstract
Saccharomyces cerevisiae has a long-standing history of biotechnological applications even before the dawn of modern biotechnology. The field is undergoing accelerated advancement with the recent systems and synthetic biology approaches. In this review, we highlight the recent findings in the field with a focus on omics studies of S. cerevisiae to investigate its stress tolerance in different industries. The latest advancements in S. cerevisiae systems and synthetic biology approaches for the development of genome-scale metabolic models (GEMs) and molecular tools such as multiplex Cas9, Cas12a, Cpf1, and Csy4 genome editing tools, modular expression cassette with optimal transcription factors, promoters, and terminator libraries as well as metabolic engineering. Omics data analysis is key to the identification of exploitable native genes/proteins/pathways in S. cerevisiae with the optimization of heterologous pathway implementation and fermentation conditions. Through systems and synthetic biology, various heterologous compound productions that require non-native biosynthetic pathways in a cell factory have been established via different strategies of metabolic engineering integrated with machine learning.
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Affiliation(s)
- Tiew-Yik Ting
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - YaDong Li
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Hamidun Bunawan
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Ahmad Bazli Ramzi
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Hoe-Han Goh
- Institute of Systems Biology, University Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
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9
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Presnell KV, Melhem O, Morse NJ, Alper HS. Modular, Synthetic Boolean Logic Gates Enabled in Saccharomyces cerevisiae through T7 Polymerases/CRISPR dCas9 Designs. ACS Synth Biol 2022; 11:3414-3425. [PMID: 36206523 DOI: 10.1021/acssynbio.2c00327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic control of gene expression, whether simply promoter selection or higher-order Boolean-style logic, is an important tool for metabolic engineering and synthetic biology. This work develops a suite of orthogonal T7 RNA polymerase systems capable of exerting AND/OR switchlike control over transcription in the yeastSaccharomyces cerevisiae. When linked with CRISPR dCas9-based regulation systems, more complex circuitry is possible including AND/OR/NAND/NOR style control in response to combinations of extracellular copper and galactose. Additionally, we demonstrate that these T7 system designs are modular and can accommodate alternative stimuli sensing as demonstrated through blue light induction. These designs should greatly reduce the time and labor necessary for developing Boolean gene circuits in yeast with novel applications including metabolic pathway control in the future.
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Affiliation(s)
- Kristin V Presnell
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Omar Melhem
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Nicholas J Morse
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton Street Stop C0400, Austin, Texas 78712, United States.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, United States
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10
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Shaw WM, Studená L, Roy K, Hapeta P, McCarty NS, Graham AE, Ellis T, Ledesma-Amaro R. Inducible expression of large gRNA arrays for multiplexed CRISPRai applications. Nat Commun 2022; 13:4984. [PMID: 36008396 PMCID: PMC9411621 DOI: 10.1038/s41467-022-32603-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 08/09/2022] [Indexed: 01/12/2023] Open
Abstract
CRISPR gene activation and inhibition (CRISPRai) has become a powerful synthetic tool for influencing the expression of native genes for foundational studies, cellular reprograming, and metabolic engineering. Here we develop a method for near leak-free, inducible expression of a polycistronic array containing up to 24 gRNAs from two orthogonal CRISPR/Cas systems to increase CRISPRai multiplexing capacity and target gene flexibility. To achieve strong inducibility, we create a technology to silence gRNA expression within the array in the absence of the inducer, since we found that long gRNA arrays for CRISPRai can express themselves even without promoter. Using this method, we create a highly tuned and easy-to-use CRISPRai toolkit in the industrially relevant yeast, Saccharomyces cerevisiae, establishing the first system to combine simultaneous activation and repression, large multiplexing capacity, and inducibility. We demonstrate this toolkit by targeting 11 genes in central metabolism in a single transformation, achieving a 45-fold increase in succinic acid, which could be precisely controlled in an inducible manner. Our method offers a highly effective way to regulate genes and rewire metabolism in yeast, with principles of gRNA array construction and inducibility that should extend to other chassis organisms.
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Affiliation(s)
- William M Shaw
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Lucie Studená
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Kyler Roy
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Piotr Hapeta
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Nicholas S McCarty
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Alicia E Graham
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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11
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Dong C, Gou Y, Lian J. SgRNA engineering for improved genome editing and expanded functional assays. Curr Opin Biotechnol 2022; 75:102697. [PMID: 35217295 DOI: 10.1016/j.copbio.2022.102697] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/27/2022] [Accepted: 02/07/2022] [Indexed: 12/22/2022]
Abstract
The CRISPR/Cas system has been established as the most powerful and practical genome engineering tool for both fundamental researches and biotechnological applications. Great efforts have been devoted to engineering the CRISPR system with better performance and novel functions. As an essential component, single guide RNAs (sgRNAs) have been extensively designed and engineered with desirable functions. This review highlights representative studies that optimize the sgRNA nucleotide sequences for improved genome editing performance (e.g. activity and specificity) as well as add extra aptamers and end extensions for expanded CRISPR-based functional assays (e.g. transcriptional regulation, genome imaging, and prime editor). The perspectives for further sgRNA engineering to establish more powerful and versatile CRISPR/Cas systems are also discussed.
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Affiliation(s)
- Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310027, China.
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12
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Shi Y, Zhang L, Zhang M, Chu J, Xia Y, Yang H, Liu L, Chen X. A CRISPR-Cas9 System-Mediated Genetic Disruption and Multi-fragment Assembly in Starmerella bombicola. ACS Synth Biol 2022; 11:1497-1509. [PMID: 35294186 DOI: 10.1021/acssynbio.1c00582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gene editing technology plays an extremely significant role in synthetic biology and metabolic engineering. Traditional genetic manipulation methods, such as homologous recombination, however, are inefficient, time-consuming, and barely feasible when disrupting multiple genes simultaneously. Starmerella bombicola, a nonconventional yeast that overproduces sophorolipids, lacks convenient genetic tools for engineering strains. Here, we developed an efficient CRISPR-Cas9 genome editing technology by combining molecular element mining and expression system optimization for S. bombicola. This CRISPR-Cas9 system improved the efficiency of gene-integration/target gene-introducing disruption by homology-directed repair and realized the multi-gene simultaneous disruptions. Based on this CRISPR-Cas9 system, we also further constructed an engineered strain via the in vivo assembly of multiple DNA fragments (10 kb) that can produce acid-type sophorolipids. These results showed that the CRISPR-Cas9 system may be an efficient and convenient strategy to perform genetic manipulation in S. bombicola.
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Affiliation(s)
- Yibo Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Lihua Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Min Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jieyu Chu
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yuanyuan Xia
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Haiquan Yang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xianzhong Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
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13
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Zhang Y, Marchisio MA. Interaction of Bare dSpCas9, Scaffold gRNA, and Type II Anti-CRISPR Proteins Highly Favors the Control of Gene Expression in the Yeast S. cerevisiae. ACS Synth Biol 2022; 11:176-190. [PMID: 34994540 DOI: 10.1021/acssynbio.1c00352] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Type II CRISPR-(d)SpCas9 and anti-CRISPR proteins (AcrIIs) show evidence of coevolution and competition for survival between bacteria and phages. In biotechnology, CRISPR-(d)SpCas9 is utilized for gene editing and transcriptional regulation. Moreover, its activity is controlled by AcrIIs. However, studies of dSpCas9/AcrII-based transcription regulation in Saccharomyces cerevisiae are rare. In this work, we used dSpCas9 as a template to engineer new transcription activators. We found that the most performant activation system requires the use of bare dSpCas9 in conjunction with scaffold gRNA (scRNA). This means that activation domains shall not be fused to dSpCas9 but rather interact with scRNA. We showed that a low amount of sgRNA is not a limiting factor in dSpCas9-driven transcription regulation. Moreover, a high quantity of sgRNA does not improve, generally, activation (and repression) efficiency. Importantly, we analyzed the performance of AcrIIA2, AcrIIA4, and AcrIIA5 in S. cerevisiae in depth. AcrIIA4 is the strongest of the three AcrIIs and also the only one able to induce high inhibition at low concentrations. However, the activation domains fused to dSpCas9 hindered interactions with the AcrIIs as well and limited their control of gene transcription regulation, confirming that bare dSpCas9 is the best solution for building synthetic genetic networks in yeast.
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Affiliation(s)
- Yadan Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
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14
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Bergenholm D, Dabirian Y, Ferreira R, Siewers V, David F, Nielsen J. Rational gRNA design based on transcription factor binding data. Synth Biol (Oxf) 2021; 6:ysab014. [PMID: 34712839 PMCID: PMC8546606 DOI: 10.1093/synbio/ysab014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/21/2021] [Accepted: 06/08/2021] [Indexed: 11/14/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system has become a standard tool in many genome engineering endeavors. The endonuclease-deficient version of Cas9 (dCas9) is also a powerful programmable tool for gene regulation. In this study, we made use of Saccharomyces cerevisiae transcription factor (TF) binding data to obtain a better understanding of the interplay between TF binding and binding of dCas9 fused to an activator domain, VPR. More specifically, we targeted dCas9–VPR toward binding sites of Gcr1–Gcr2 and Tye7 present in several promoters of genes encoding enzymes engaged in the central carbon metabolism. From our data, we observed an upregulation of gene expression when dCas9–VPR was targeted next to a TF binding motif, whereas a downregulation or no change was observed when dCas9 was bound on a TF motif. This suggests a steric competition between dCas9 and the specific TF. Integrating TF binding data, therefore, proved to be useful for designing guide RNAs for CRISPR interference or CRISPR activation applications.
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Affiliation(s)
- David Bergenholm
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Yasaman Dabirian
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Florian David
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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15
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CRAGE-CRISPR facilitates rapid activation of secondary metabolite biosynthetic gene clusters in bacteria. Cell Chem Biol 2021; 29:696-710.e4. [PMID: 34508657 DOI: 10.1016/j.chembiol.2021.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/19/2021] [Accepted: 08/20/2021] [Indexed: 12/31/2022]
Abstract
With the advent of genome sequencing and mining technologies, secondary metabolite biosynthetic gene clusters (BGCs) within bacterial genomes are becoming easier to predict. For subsequent BGC characterization, clustered regularly interspaced short palindromic repeats (CRISPR) has contributed to knocking out target genes and/or modulating their expression; however, CRISPR is limited to strains for which robust genetic tools are available. Here we present a strategy that combines CRISPR with chassis-independent recombinase-assisted genome engineering (CRAGE), which enables CRISPR systems in diverse bacteria. To demonstrate CRAGE-CRISPR, we select 10 polyketide/non-ribosomal peptide BGCs in Photorhabdus luminescens as models and create their deletion and activation mutants. Subsequent loss- and gain-of-function studies confirm 22 secondary metabolites associated with the BGCs, including a metabolite from a previously uncharacterized BGC. These results demonstrate that the CRAGE-CRISPR system is a simple yet powerful approach to rapidly perturb expression of defined BGCs and to profile genotype-phenotype relationships in bacteria.
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16
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Chang D, Hirate T, Uehara C, Maruyama H, Uozumi N, Arai F. Evaluating Young's Modulus of Single Yeast Cells Based on Compression Using an Atomic Force Microscope with a Flat Tip. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2021; 27:392-399. [PMID: 33446296 DOI: 10.1017/s1431927620024903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
In this research, atomic force microscopy (AFM) with a flat tip cantilever is utilized to measure Young's modulus of a whole yeast cell (Saccharomyces cerevisiae BY4741). The results acquired from AFM are similar to those obtained using a microfluidic chip compression system. The mechanical properties of single yeast cells are important parameters which can be examined using AFM. Conventional studies apply AFM with a sharp cantilever tip to indent the cell and measure the force-indentation curve, from which Young's modulus can be calculated. However, sharp tips introduce problems because the shape variation can lead to a different result and cannot represent the stiffness of the whole cell. It can lead to a lack of broader meaning when evaluating Young's modulus of yeast cells. In this report, we confirm the differences in results obtained when measuring the compression of a poly(dimethylsiloxane) bead using a commercial sharp tip versus a unique flat tip. The flat tip effectively avoids tip-derived errors, so we use this method to compress whole yeast cells and generate a force–deformation curve. We believe our proposed method is effective for evaluating Young's modulus of whole yeast cells.
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Affiliation(s)
- Di Chang
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Room 108, Aerospace Mechanical Engineering Research Building, Furo-cho, Chikusa-ku, Nagoya, Aichi464-8603, Japan
| | - Takahiro Hirate
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Room 108, Aerospace Mechanical Engineering Research Building, Furo-cho, Chikusa-ku, Nagoya, Aichi464-8603, Japan
| | - Chihiro Uehara
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai980-8579, Japan
| | - Hisataka Maruyama
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Room 108, Aerospace Mechanical Engineering Research Building, Furo-cho, Chikusa-ku, Nagoya, Aichi464-8603, Japan
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai980-8579, Japan
| | - Fumihito Arai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Room 108, Aerospace Mechanical Engineering Research Building, Furo-cho, Chikusa-ku, Nagoya, Aichi464-8603, Japan
- Department of Mechanical Engineering, The University of Tokyo, Tokyo113-8654, Japan
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17
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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.
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18
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Misa J, Schwartz C. CRISPR Interference and Activation to Modulate Transcription in Yarrowia lipolytica. Methods Mol Biol 2021; 2307:95-109. [PMID: 33847984 DOI: 10.1007/978-1-0716-1414-3_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Recent developments in RNA-guided nuclease technologies have advanced the engineering of a wide range of organisms, including the nonconventional yeast Yarrowia lipolytica. Y. lipolytica has been the focus of a range of synthetic biology and metabolic engineering studies due to its high capacity to synthesize and accumulate intracellular lipids. The CRISPR-Cas9 system from Streptococcus pyogenes has been successfully adapted and used for genome editing in Y. lipolytica. However, as engineered strains are moved closer to industrialization, the need for finer control of transcription is still present. To overcome this challenge, we have developed CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) systems to allow modulating the transcription of endogenous genes. We begin this protocol chapter by describing how to use the CRISPRi system to repress expression of any gene in Y. lipolytica. A second method describes how to use the CRISPRa system to increase expression of native Y. lipolytica genes. Finally, we describe how CRISPRi or CRISPRa vectors can be combined to enable multiplexed activation or repression of more than one gene. The implementation of CRISPRi and CRISPRa systems improves our ability to control gene expression in Y. lipolytica and promises to enable more advanced synthetic biology and metabolic engineering studies in this host.
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Affiliation(s)
- Joshua Misa
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA
| | - Cory Schwartz
- Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA.
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19
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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.
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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.
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20
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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.
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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
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21
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Adiego-Pérez B, Randazzo P, Daran JM, Verwaal R, Roubos JA, Daran-Lapujade P, van der Oost J. Multiplex genome editing of microorganisms using CRISPR-Cas. FEMS Microbiol Lett 2020; 366:5489186. [PMID: 31087001 PMCID: PMC6522427 DOI: 10.1093/femsle/fnz086] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/10/2019] [Indexed: 12/13/2022] Open
Abstract
Microbial production of chemical compounds often requires highly engineered microbial cell factories. During the last years, CRISPR-Cas nucleases have been repurposed as powerful tools for genome editing. Here, we briefly review the most frequently used CRISPR-Cas tools and describe some of their applications. We describe the progress made with respect to CRISPR-based multiplex genome editing of industrial bacteria and eukaryotic microorganisms. We also review the state of the art in terms of gene expression regulation using CRISPRi and CRISPRa. Finally, we summarize the pillars for efficient multiplexed genome editing and present our view on future developments and applications of CRISPR-Cas tools for multiplex genome editing.
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Affiliation(s)
- Belén Adiego-Pérez
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Paola Randazzo
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - René Verwaal
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Johannes A Roubos
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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22
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McCarty NS, Graham AE, Studená L, Ledesma-Amaro R. Multiplexed CRISPR technologies for gene editing and transcriptional regulation. Nat Commun 2020; 11:1281. [PMID: 32152313 PMCID: PMC7062760 DOI: 10.1038/s41467-020-15053-x] [Citation(s) in RCA: 241] [Impact Index Per Article: 60.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 02/17/2020] [Indexed: 12/18/2022] Open
Abstract
Multiplexed CRISPR technologies, in which numerous gRNAs or Cas enzymes are expressed at once, have facilitated powerful biological engineering applications, vastly enhancing the scope and efficiencies of genetic editing and transcriptional regulation. In this review, we discuss multiplexed CRISPR technologies and describe methods for the assembly, expression and processing of synthetic guide RNA arrays in vivo. Applications that benefit from multiplexed CRISPR technologies, including cellular recorders, genetic circuits, biosensors, combinatorial genetic perturbations, large-scale genome engineering and the rewiring of metabolic pathways, are highlighted. We also offer a glimpse of emerging challenges and emphasize experimental considerations for future studies.
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Affiliation(s)
- Nicholas S McCarty
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alicia E Graham
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Lucie Studená
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK.
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23
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Lian J, Schultz C, Cao M, HamediRad M, Zhao H. Multi-functional genome-wide CRISPR system for high throughput genotype-phenotype mapping. Nat Commun 2019; 10:5794. [PMID: 31857575 PMCID: PMC6923430 DOI: 10.1038/s41467-019-13621-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 11/12/2019] [Indexed: 01/20/2023] Open
Abstract
Genome-scale engineering is an indispensable tool to understand genome functions due to our limited knowledge of cellular networks. Unfortunately, most existing methods for genome-wide genotype–phenotype mapping are limited to a single mode of genomic alteration, i.e. overexpression, repression, or deletion. Here we report a multi-functional genome-wide CRISPR (MAGIC) system to precisely control the expression level of defined genes to desired levels throughout the whole genome. By combining the tri-functional CRISPR system and array-synthesized oligo pools, MAGIC is used to create, to the best of our knowledge, one of the most comprehensive and diversified genomic libraries in yeast ever reported. The power of MAGIC is demonstrated by the identification of previously uncharacterized genetic determinants of complex phenotypes, particularly those having synergistic interactions when perturbed to different expression levels. MAGIC represents a powerful synthetic biology tool to investigate fundamental biological questions as well as engineer complex phenotypes for biotechnological applications. Genome-scale engineering is generally limited to single methods of alteration such as overexpression, repression or deletion. Here the authors present a tri-functional CRISPR system that can engineer complex synergistic interactions in a genome-wide manner.
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Affiliation(s)
- Jiazhang Lian
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, 310027, Hangzhou, China
| | - Carl Schultz
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mingfeng Cao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Lifefoundry Inc., 60 Hazelwood Dr., Champaign, IL, 61820, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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24
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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.
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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
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25
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Payen C, Thompson D. The renaissance of yeasts as microbial factories in the modern age of biomanufacturing. Yeast 2019; 36:685-700. [DOI: 10.1002/yea.3439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/09/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022] Open
Affiliation(s)
- Celia Payen
- DuPont Nutrition and Biosciences Wilmington Delaware
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26
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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.
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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
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27
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Geller SH, Antwi EB, Di Ventura B, McClean MN. Optogenetic Repressors of Gene Expression in Yeasts Using Light-Controlled Nuclear Localization. Cell Mol Bioeng 2019; 12:511-528. [PMID: 31719930 PMCID: PMC6816687 DOI: 10.1007/s12195-019-00598-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 09/03/2019] [Indexed: 01/30/2023] Open
Abstract
INTRODUCTION Controlling gene expression is a fundamental goal of basic and synthetic biology because it allows insight into cellular function and control of cellular activity. We explored the possibility of generating an optogenetic repressor of gene expression in the model organism Saccharomyces cerevisiae by using light to control the nuclear localization of nuclease-dead Cas9, dCas9. METHODS The dCas9 protein acts as a repressor for a gene of interest when localized to the nucleus in the presence of an appropriate guide RNA (sgRNA). We engineered dCas9, the mammalian transcriptional repressor Mxi1, and an optogenetic tool to control nuclear localization (LINuS) as parts in an existing yeast optogenetic toolkit. This allowed expression cassettes containing novel dCas9 repressor configurations and guide RNAs to be rapidly constructed and integrated into yeast. RESULTS Our library of repressors displays a range of basal repression without the need for inducers or promoter modification. Populations of cells containing these repressors can be combined to generate a heterogeneous population of yeast with a 100-fold expression range. We find that repression can be dialed modestly in a light dose- and intensity-dependent manner. We used this library to repress expression of the lanosterol 14-alpha-demethylase Erg11, generating yeast with a range of sensitivity to the important antifungal drug fluconazole. CONCLUSIONS This toolkit will be useful for spatiotemporal perturbation of gene expression in Saccharomyces cerevisiae. Additionally, we believe that the simplicity of our scheme will allow these repressors to be easily modified to control gene expression in medically relevant fungi, such as pathogenic yeasts.
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Affiliation(s)
- Stephanie H. Geller
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1550 Engineering Drive, Madison, WI 53706 USA
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, 1525 Linden Dr., Madison, WI 53706 USA
| | - Enoch B. Antwi
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
- Heidelberg Biosciences International Graduate School (HBIGS), 69120 Heidelberg, Germany
| | - Barbara Di Ventura
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany
| | - Megan N. McClean
- Department of Biomedical Engineering, University of Wisconsin-Madison, 1550 Engineering Drive, Madison, WI 53706 USA
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Hofmann A, Falk J, Prangemeier T, Happel D, Köber A, Christmann A, Koeppl H, Kolmar H. A tightly regulated and adjustable CRISPR-dCas9 based AND gate in yeast. Nucleic Acids Res 2019; 47:509-520. [PMID: 30476163 PMCID: PMC6326796 DOI: 10.1093/nar/gky1191] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/19/2018] [Indexed: 02/07/2023] Open
Abstract
The robust and precise on and off switching of one or more genes of interest, followed by expression or repression is essential for many biological circuits as well as for industrial applications. However, many regulated systems published to date influence the viability of the host cell, show high basal expression or enable only the overexpression of the target gene without the possibility of fine regulation. Herein, we describe an AND gate designed to overcome these limitations by combining the advantages of three well established systems, namely the scaffold RNA CRISPR/dCas9 platform that is controlled by Gal10 as a natural and by LexA-ER-AD as heterologous transcription factor. We hence developed a predictable and modular, versatile expression control system. The selection of a reporter gene set up combining a gene of interest (GOI) with a fluorophore by the ribosomal skipping T2A sequence allows to adapt the system to any gene of interest without losing reporter function. In order to obtain a better understanding of the underlying principles and the functioning of our system, we backed our experimental findings with the development of a mathematical model and single-cell analysis.
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Affiliation(s)
- Anja Hofmann
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Johannes Falk
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, 64289 Darmstadt, Germany
| | - Tim Prangemeier
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Dominic Happel
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Adrian Köber
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Andreas Christmann
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinz Koeppl
- Department of Electrical Engineering and Information Technology, Technische Universität Darmstadt, 64283 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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Zhang Y, Malzahn AA, Sretenovic S, Qi Y. The emerging and uncultivated potential of CRISPR technology in plant science. NATURE PLANTS 2019; 5:778-794. [PMID: 31308503 DOI: 10.1038/s41477-019-0461-5] [Citation(s) in RCA: 207] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 05/24/2019] [Indexed: 05/18/2023]
Abstract
The application of clustered regularly interspaced short palindromic repeats (CRISPR) for genetic manipulation has revolutionized life science over the past few years. CRISPR was first discovered as an adaptive immune system in bacteria and archaea, and then engineered to generate targeted DNA breaks in living cells and organisms. During the cellular DNA repair process, various DNA changes can be introduced. The diverse and expanding CRISPR toolbox allows programmable genome editing, epigenome editing and transcriptome regulation in plants. However, challenges in plant genome editing need to be fully appreciated and solutions explored. This Review intends to provide an informative summary of the latest developments and breakthroughs of CRISPR technology, with a focus on achievements and potential utility in plant biology. Ultimately, CRISPR will not only facilitate basic research, but also accelerate plant breeding and germplasm development. The application of CRISPR to improve germplasm is particularly important in the context of global climate change as well as in the face of current agricultural, environmental and ecological challenges.
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Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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30
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Gene expression engineering in fungi. Curr Opin Biotechnol 2019; 59:141-149. [PMID: 31154079 DOI: 10.1016/j.copbio.2019.04.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/27/2019] [Accepted: 04/24/2019] [Indexed: 02/03/2023]
Abstract
Fungi are a highly diverse group of microbial species that possess a plethora of biotechnologically useful metabolic and physiological properties. Important enablers for fungal biology studies and their biotechnological use are well-performing gene expression tools. Different types of gene expression tools exist; however, typically they are at best only functional in one or a few closely related species. This has hampered research and development of industrially relevant production systems. Here, we review operational principles and concepts of fungal gene expression tools. We present an overview on tools that utilize endogenous fungal promoters and modified hybrid expression systems composed of engineered promoters and transcription factors. Finally, we review synthetic expression tools that are functional across a broad range of fungal species.
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31
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Xia P, Ling H, Foo JL, Chang MW. Synthetic Biology Toolkits for Metabolic Engineering of Cyanobacteria. Biotechnol J 2019; 14:e1800496. [DOI: 10.1002/biot.201800496] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/19/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Peng‐Fei Xia
- Department of Biochemistry Yong Loo Lin School of MedicineNational University of Singapore8 Medical Drive Singapore 117597 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of Singapore28 Medical Drive Singapore 117456 Singapore
| | - Hua Ling
- Department of Biochemistry Yong Loo Lin School of MedicineNational University of Singapore8 Medical Drive Singapore 117597 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of Singapore28 Medical Drive Singapore 117456 Singapore
| | - Jee Loon Foo
- Department of Biochemistry Yong Loo Lin School of MedicineNational University of Singapore8 Medical Drive Singapore 117597 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of Singapore28 Medical Drive Singapore 117456 Singapore
| | - Matthew Wook Chang
- Department of Biochemistry Yong Loo Lin School of MedicineNational University of Singapore8 Medical Drive Singapore 117597 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI)National University of Singapore28 Medical Drive Singapore 117456 Singapore
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32
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Yang J, Kim B, Kim GY, Jung GY, Seo SW. Synthetic biology for evolutionary engineering: from perturbation of genotype to acquisition of desired phenotype. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:113. [PMID: 31086565 PMCID: PMC6506968 DOI: 10.1186/s13068-019-1460-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
With the increased attention on bio-based industry, demands for techniques that enable fast and effective strain improvement have been dramatically increased. Evolutionary engineering, which is less dependent on biological information, has been applied to strain improvement. Currently, synthetic biology has made great innovations in evolutionary engineering, particularly in the development of synthetic tools for phenotypic perturbation. Furthermore, discovering biological parts with regulatory roles and devising novel genetic circuits have promoted high-throughput screening and selection. In this review, we first briefly explain basics of synthetic biology tools for mutagenesis and screening of improved variants, and then describe how these strategies have been improved and applied to phenotypic engineering. Evolutionary engineering using advanced synthetic biology tools will enable further innovation in phenotypic engineering through the development of novel genetic parts and assembly into well-designed logic circuits that perform complex tasks.
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Affiliation(s)
- Jina Yang
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
- Institute of Chemical Process, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Beomhee Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Gi Yeon Kim
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
| | - Gyoo Yeol Jung
- Department of Chemical Engineering and School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673 South Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
- Institute of Chemical Process, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826 South Korea
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Xia PF, Ling H, Foo JL, Chang MW. Synthetic genetic circuits for programmable biological functionalities. Biotechnol Adv 2019; 37:107393. [PMID: 31051208 DOI: 10.1016/j.biotechadv.2019.04.015] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 02/06/2023]
Abstract
Living organisms evolve complex genetic networks to interact with the environment. Due to the rapid development of synthetic biology, various modularized genetic parts and units have been identified from these networks. They have been employed to construct synthetic genetic circuits, including toggle switches, oscillators, feedback loops and Boolean logic gates. Building on these circuits, complex genetic machines with capabilities in programmable decision-making could be created. Consequently, these accomplishments have led to novel applications, such as dynamic and autonomous modulation of metabolic networks, directed evolution of biological units, remote and targeted diagnostics and therapies, as well as biological containment methods to prevent release of engineered microorganisms and genetic materials. Herein, we outline the principles in genetic circuit design that have initiated a new chapter in transforming concepts to realistic applications. The features of modularized building blocks and circuit architecture that facilitate realization of circuits for a variety of novel applications are discussed. Furthermore, recent advances and challenges in employing genetic circuits to impart microorganisms with distinct and programmable functionalities are highlighted. We envision that this review gives new insights into the design of synthetic genetic circuits and offers a guideline for the implementation of different circuits in various aspects of biotechnology and bioengineering.
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Affiliation(s)
- Peng-Fei Xia
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Hua Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jee Loon Foo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
| | - Matthew Wook Chang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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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.
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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
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35
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Lian J, Mishra S, Zhao H. Recent advances in metabolic engineering of Saccharomyces cerevisiae: New tools and their applications. Metab Eng 2018; 50:85-108. [DOI: 10.1016/j.ymben.2018.04.011] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 10/17/2022]
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36
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Deaner M, Holzman A, Alper HS. Modular Ligation Extension of Guide RNA Operons (LEGO) for Multiplexed dCas9 Regulation of Metabolic Pathways in Saccharomyces cerevisiae. Biotechnol J 2018; 13:e1700582. [PMID: 29663663 DOI: 10.1002/biot.201700582] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/23/2018] [Indexed: 02/01/2023]
Abstract
Metabolic engineering typically utilizes a suboptimal step-wise gene target optimization approach to parse a highly connected and regulated cellular metabolism. While the endonuclease-null CRISPR/Cas system has enabled gene expression perturbations without genetic modification, it has been mostly limited to small sets of gene targets in eukaryotes due to inefficient methods to assemble and express large sgRNA operons. In this work, we develop a TEF1p-tRNA expression system and demonstrate that the use of tRNAs as splicing elements flanking sgRNAs provides higher efficiency than both Pol III and ribozyme-based expression across a variety of single sgRNA and multiplexed contexts. Next, we devise and validate a scheme to allow modular construction of tRNA-sgRNA (TST) operons using an iterative Type IIs digestion/ligation extension approach, termed CRISPR-Ligation Extension of sgRNA Operons (LEGO). This approach enables facile construction of large TST operons. We demonstrate this utility by constructing a metabolic rewiring prototype for 2,3-butanediol production in 2 distinct yeast strain backgrounds. These results demonstrate that our approach can act as a surrogate for traditional genetic modification on a much shorter design-cycle timescale.
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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
| | - Allison Holzman
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712
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Li J, Xu Z, Chupalov A, Marchisio MA. Anti-CRISPR-based biosensors in the yeast S. cerevisiae. J Biol Eng 2018; 12:11. [PMID: 30123320 PMCID: PMC6090965 DOI: 10.1186/s13036-018-0101-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/04/2018] [Indexed: 02/07/2023] Open
Abstract
Background Anti-CRISPR proteins are expressed by phages as a reaction to the bacterial CRISPR–Cas defense system. Recently, the structures of anti-CRISPR proteins have been determined, and their diverse functions have been clarified. Anti-CRISPR proteins such as LmAcrIIA2 and LmAcrIIA4 interact with the SpCas9:gRNA system and occlude the protospacer adjacent motif (PAM) recognition site, thereby preventing SpCas9:gRNA from binding to the DNA. Hence, anti-CRISPR proteins represent a powerful means to control and modulate the activity of SpCas9 and its nuclease-deficient version dSpCas9. LmAcrIIA2 and LmAcrIIA4 have been shown to be efficient inhibitors of SpCas9 in Escherichia coli, Saccharomyces cerevisiae, and mammalian cells. To date, there have been no reports of anti-CRISPR-based synthetic gene circuits engineered into yeast cells. Results We constructed in the yeast S. cerevisiae synthetic biosensors based on the anti-CRISPR–dSpCas9:gRNA interaction. Upon induction with galactose or β-estradiol, anti-CRISPR proteins (LmAcrIIA4, LmAcrIIA2, and StAcrIIA5) produced an enhancement in fluorescence expression by preventing the dSpCas9–Mxi1:gRNA complex from binding to the DNA. We found that LmAcrIIA2 performed as well as LmAcrIIA4 in S. cerevisiae, whereas StAcrIIA5, which had previously been tested in bacteria only, had non-negligible negative effects on yeast cell growth. The efficiency of anti-CRISPR-based biosensors was strongly dependent on the means by which the guide RNAs were produced. The best performance, as measured by the increase in fluorescence, was achieved using a “ribozyme–gRNA–ribozyme” expression cassette under the control of the yeast constitutive ADH1 promoter. Conclusions This work demonstrates that anti-CRISPR proteins are effective dSpCas9 suppressors in yeast cells. In particular, LmAcrIIA2 and LmAcrIIA4 could be employed as new components of yeast synthetic gene circuits. Electronic supplementary material The online version of this article (10.1186/s13036-018-0101-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jing Li
- School of Life Science and Technology, 2 Yikuang Street, Nan Gang DistrictHarbin, 150080 People's Republic of China
| | - Zengliang Xu
- School of Life Science and Technology, 2 Yikuang Street, Nan Gang DistrictHarbin, 150080 People's Republic of China
| | - Aleksandr Chupalov
- School of Life Science and Technology, 2 Yikuang Street, Nan Gang DistrictHarbin, 150080 People's Republic of China
| | - Mario Andrea Marchisio
- School of Life Science and Technology, 2 Yikuang Street, Nan Gang DistrictHarbin, 150080 People's Republic of China
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Fontana J, Voje WE, Zalatan JG, Carothers JM. Prospects for engineering dynamic CRISPR–Cas transcriptional circuits to improve bioproduction. ACTA ACUST UNITED AC 2018; 45:481-490. [DOI: 10.1007/s10295-018-2039-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/26/2018] [Indexed: 12/26/2022]
Abstract
Abstract
Dynamic control of gene expression is emerging as an important strategy for controlling flux in metabolic pathways and improving bioproduction of valuable compounds. Integrating dynamic genetic control tools with CRISPR–Cas transcriptional regulation could significantly improve our ability to fine-tune the expression of multiple endogenous and heterologous genes according to the state of the cell. In this mini-review, we combine an analysis of recent literature with examples from our own work to discuss the prospects and challenges of developing dynamically regulated CRISPR–Cas transcriptional control systems for applications in synthetic biology and metabolic engineering.
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Affiliation(s)
- Jason Fontana
- 0000000122986657 grid.34477.33 Molecular Engineering and Sciences Institute and Center for Synthetic Biology University of Washington 98195 Seattle WA USA
| | - William E Voje
- 0000000122986657 grid.34477.33 Molecular Engineering and Sciences Institute and Center for Synthetic Biology University of Washington 98195 Seattle WA USA
- 0000000122986657 grid.34477.33 Department of Chemical Engineering University of Washington 98195 Seattle WA USA
| | - Jesse G Zalatan
- 0000000122986657 grid.34477.33 Molecular Engineering and Sciences Institute and Center for Synthetic Biology University of Washington 98195 Seattle WA USA
- 0000000122986657 grid.34477.33 Department of Chemistry University of Washington 98195 Seattle WA USA
| | - James M Carothers
- 0000000122986657 grid.34477.33 Molecular Engineering and Sciences Institute and Center for Synthetic Biology University of Washington 98195 Seattle WA USA
- 0000000122986657 grid.34477.33 Department of Chemical Engineering University of Washington 98195 Seattle WA USA
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Rantasalo A, Kuivanen J, Penttilä M, Jäntti J, Mojzita D. Synthetic Toolkit for Complex Genetic Circuit Engineering in Saccharomyces cerevisiae. ACS Synth Biol 2018; 7:1573-1587. [PMID: 29750501 PMCID: PMC6150731 DOI: 10.1021/acssynbio.8b00076] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Sustainable production of chemicals, materials, and pharmaceuticals is increasingly performed by genetically engineered cell factories. Engineering of complex metabolic routes or cell behavior control systems requires robust and predictable gene expression tools. In this challenging task, orthogonality is a fundamental prerequisite for such tools. In this study, we developed and characterized in depth a comprehensive gene expression toolkit that allows accurate control of gene expression in Saccharomyces cerevisiae without marked interference with native cellular regulation. The toolkit comprises a set of transcription factors, designed to function as synthetic activators or repressors, and transcription-factor-dependent promoters, which together provide a broad expression range surpassing, at high end, the strongest native promoters. Modularity of the developed tools is demonstrated by establishing a novel bistable genetic circuit with robust performance to control a heterologous metabolic pathway and enabling on-demand switching between two alternative metabolic branches.
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Affiliation(s)
- Anssi Rantasalo
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Joosu Kuivanen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Merja Penttilä
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Jussi Jäntti
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
| | - Dominik Mojzita
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044 VTT Espoo, Finland
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40
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Jensen MK. Design principles for nuclease-deficient CRISPR-based transcriptional regulators. FEMS Yeast Res 2018; 18:4966988. [PMID: 29726937 PMCID: PMC5932555 DOI: 10.1093/femsyr/foy039] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 04/06/2018] [Indexed: 12/18/2022] Open
Abstract
The engineering of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR-associated proteins continues to expand the toolkit available for genome editing, reprogramming gene regulation, genome visualisation and epigenetic studies of living organisms. In this review, the emerging design principles on the use of nuclease-deficient CRISPR-based reprogramming of gene expression will be presented. The review will focus on the designs implemented in yeast both at the level of CRISPR proteins and guide RNA (gRNA), but will lend due credits to the seminal studies performed in other species where relevant. In addition to design principles, this review also highlights applications benefitting from the use of CRISPR-mediated transcriptional regulation and discusses the future directions to further expand the toolkit for nuclease-deficient reprogramming of genomes. As such, this review should be of general interest for experimentalists to get familiarised with the parameters underlying the power of reprogramming genomic functions by use of nuclease-deficient CRISPR technologies.
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Affiliation(s)
- Michael K Jensen
- Novo Nordisk Foundation, Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kgs. Lyngby 2800, Denmark
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41
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Juergens H, Varela JA, Gorter de Vries AR, Perli T, Gast VJM, Gyurchev NY, Rajkumar AS, Mans R, Pronk JT, Morrissey JP, Daran JMG. Genome editing in Kluyveromyces and Ogataea yeasts using a broad-host-range Cas9/gRNA co-expression plasmid. FEMS Yeast Res 2018; 18:4847887. [PMID: 29438517 PMCID: PMC6018904 DOI: 10.1093/femsyr/foy012] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/08/2018] [Indexed: 12/17/2022] Open
Abstract
While CRISPR-Cas9-mediated genome editing has transformed yeast research, current plasmids and cassettes for Cas9 and guide-RNA expression are species specific. CRISPR tools that function in multiple yeast species could contribute to the intensifying research on non-conventional yeasts. A plasmid carrying a pangenomic origin of replication and two constitutive expression cassettes for Cas9 and ribozyme-flanked gRNAs was constructed. Its functionality was tested by analyzing inactivation of the ADE2 gene in four yeast species. In two Kluyveromyces species, near-perfect targeting (≥96%) and homologous repair (HR) were observed in at least 24% of transformants. In two Ogataea species, Ade- mutants were not observed directly after transformation, but prolonged incubation of transformed cells resulted in targeting efficiencies of 9% to 63% mediated by non-homologous end joining (NHEJ). In an Ogataea parapolymorpha ku80 mutant, deletion of OpADE2 mediated by HR was achieved, albeit at low efficiencies (<1%). Furthermore the expression of a dual polycistronic gRNA array enabled simultaneous interruption of OpADE2 and OpYNR1 demonstrating flexibility of ribozyme-flanked gRNA design for multiplexing. While prevalence of NHEJ prevented HR-mediated editing in Ogataea, such targeted editing was possible in Kluyveromyces. This broad-host-range CRISPR/gRNA system may contribute to exploration of Cas9-mediated genome editing in other Saccharomycotina yeasts.
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Affiliation(s)
- Hannes Juergens
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Javier A Varela
- School of Microbiology/Centre for Synthetic Biology and Biotechnology/Environmental Research Institute/APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - Arthur R Gorter de Vries
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Thomas Perli
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Veronica J M Gast
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Nikola Y Gyurchev
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Arun S Rajkumar
- School of Microbiology/Centre for Synthetic Biology and Biotechnology/Environmental Research Institute/APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - John P Morrissey
- School of Microbiology/Centre for Synthetic Biology and Biotechnology/Environmental Research Institute/APC Microbiome Institute, University College Cork, Cork T12 YN60, Ireland
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
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42
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Morse NJ, Wagner JM, Reed KB, Gopal MR, Lauffer LH, Alper HS. T7 Polymerase Expression of Guide RNAs in vivo Allows Exportable CRISPR-Cas9 Editing in Multiple Yeast Hosts. ACS Synth Biol 2018; 7:1075-1084. [PMID: 29565571 DOI: 10.1021/acssynbio.7b00461] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Efficient guide RNA expression often limits CRISPR-Cas9 implementation in new hosts. To address this limitation in fungal systems, we demonstrate the utility of a T7 polymerase system to effectively express sgRNAs. Initially, we developed a methodology in Saccharomyces cerevisiae using a modified version of the T7 P266L mutant polymerase with an SV40 nuclear localization signal to allow guide RNA expression immediately downstream of a T7 promoter. To improve targeting efficiency, guide RNA design was found to be tolerant to three mismatches or up to three additional bases appended to the 5' end. The addition of three guanines to a T7-based guide RNA improved guide RNA expression 80-fold and achieved transcriptional output similar to the strong Pol III snr52 promoter. Resulting gene editing and dCas9-guided gene regulation with a T7-based guide RNA was on par with the commonly used snr52 system in S. cerevisiae. Finally, 96% and 60% genome editing efficiencies were achieved in Kluyveromyces lactis and Yarrowia lipolytica respectively with minimal optimization of this system. Thus, T7-based expression of sgRNAs offers an orthogonal method for implementing CRISPR systems in fungal systems.
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Affiliation(s)
- Nicholas J Morse
- McKetta Department of Chemical Engineering , The University of Texas at Austin , 200 E Dean Keeton Street Stop C0400 , Austin , Texas 78712 , United States
| | - James M Wagner
- McKetta Department of Chemical Engineering , The University of Texas at Austin , 200 E Dean Keeton Street Stop C0400 , Austin , Texas 78712 , United States
| | - Kevin B Reed
- McKetta Department of Chemical Engineering , The University of Texas at Austin , 200 E Dean Keeton Street Stop C0400 , Austin , Texas 78712 , United States
| | - Madan R Gopal
- McKetta Department of Chemical Engineering , The University of Texas at Austin , 200 E Dean Keeton Street Stop C0400 , Austin , Texas 78712 , United States
| | - Lars H Lauffer
- McKetta Department of Chemical Engineering , The University of Texas at Austin , 200 E Dean Keeton Street Stop C0400 , Austin , Texas 78712 , United States
| | - Hal S Alper
- McKetta Department of Chemical Engineering , The University of Texas at Austin , 200 E Dean Keeton Street Stop C0400 , Austin , Texas 78712 , United States
- Institute for Cellular and Molecular Biology , The University of Texas at Austin , 2500 Speedway Avenue , Austin , Texas 78712 , United States
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43
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Lian J, HamediRad M, Zhao H. Advancing Metabolic Engineering of Saccharomyces cerevisiae Using the CRISPR/Cas System. Biotechnol J 2018; 13:e1700601. [PMID: 29436783 DOI: 10.1002/biot.201700601] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/22/2018] [Indexed: 12/20/2022]
Abstract
Thanks to its ease of use, modularity, and scalability, the clustered regularly interspaced short palindromic repeats (CRISPR) system has been increasingly used in the design and engineering of Saccharomyces cerevisiae, one of the most popular hosts for industrial biotechnology. This review summarizes the recent development of this disruptive technology for metabolic engineering applications, including CRISPR-mediated gene knock-out and knock-in as well as transcriptional activation and interference. More importantly, multi-functional CRISPR systems that combine both gain- and loss-of-function modulations for combinatorial metabolic engineering are highlighted.
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Affiliation(s)
- Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.,Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL 61801, United States
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, UrbanaIL 61801, United States.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana,IL 61801, United States
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44
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Misa J, Schwartz C, Wheeldon I. Design of Hybrid RNA Polymerase III Promoters for Efficient CRISPR-Cas9 Function. Bio Protoc 2018; 8:e2779. [PMID: 34179292 DOI: 10.21769/bioprotoc.2779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 11/02/2022] Open
Abstract
The discovery of the CRISPR-Cas9 system from Streptococcus pyogenes has allowed the development of genome engineering tools in a variety of organisms. A frequent limitation in CRISPR-Cas9 function is adequate expression levels of sgRNA. This protocol provides a strategy to construct hybrid RNA polymerase III (Pol III) promoters that facilitate high expression of sgRNA and improved CRISPR-Cas9 function. We provide selection criteria of Pol III promoters, efficient promoter construction methods, and a sample screening technique to test the efficiency of the hybrid promoters. A hybrid promoter system developed for Yarrowia lipolytica will serve as a model.
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Affiliation(s)
- Joshua Misa
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, United States
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, United States
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, United States
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45
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DeLorenzo DM, Rottinghaus AG, Henson WR, Moon TS. Molecular Toolkit for Gene Expression Control and Genome Modification in Rhodococcus opacus PD630. ACS Synth Biol 2018; 7:727-738. [PMID: 29366319 DOI: 10.1021/acssynbio.7b00416] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rhodococcus opacus PD630 is a non-model Gram-positive bacterium that possesses desirable traits for lignocellulosic biomass conversion. In particular, it has a relatively rapid growth rate, exhibits genetic tractability, produces high quantities of lipids, and can tolerate and consume toxic lignin-derived aromatic compounds. Despite these unique, industrially relevant characteristics, R. opacus has been underutilized because of a lack of reliable genetic parts and engineering tools. In this work, we developed a molecular toolbox for reliable gene expression control and genome modification in R. opacus. To facilitate predictable gene expression, a constitutive promoter library spanning ∼45-fold in output was constructed. To improve the characterization of available plasmids, the copy numbers of four heterologous and nine endogenous plasmids were determined using quantitative PCR. The molecular toolbox was further expanded by screening a previously unreported antibiotic resistance marker (HygR) and constructing a curable plasmid backbone for temporary gene expression (pB264). Furthermore, a system for genome modification was devised, and three neutral integration sites were identified using a novel combination of transcriptomic data, genomic architecture, and growth rate analysis. Finally, the first reported system for targeted, tunable gene repression in Rhodococcus was developed by utilizing CRISPR interference (CRISPRi). Overall, this work greatly expands the ability to manipulate and engineer R. opacus, making it a viable new chassis for bioproduction from renewable feedstocks.
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Affiliation(s)
- Drew M. DeLorenzo
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Austin G. Rottinghaus
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - William R. Henson
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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46
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Ferreira R, David F, Nielsen J. Advancing biotechnology with CRISPR/Cas9: recent applications and patent landscape. J Ind Microbiol Biotechnol 2018; 45:467-480. [PMID: 29362972 DOI: 10.1007/s10295-017-2000-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/19/2017] [Indexed: 12/24/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) is poised to become one of the key scientific discoveries of the twenty-first century. Originating from prokaryotic and archaeal immune systems to counter phage invasions, CRISPR-based applications have been tailored for manipulating a broad range of living organisms. From the different elucidated types of CRISPR mechanisms, the type II system adapted from Streptococcus pyogenes has been the most exploited as a tool for genome engineering and gene regulation. In this review, we describe the different applications of CRISPR/Cas9 technology in the industrial biotechnology field. Next, we detail the current status of the patent landscape, highlighting its exploitation through different companies, and conclude with future perspectives of this technology.
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Affiliation(s)
- Raphael Ferreira
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Göteborg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Göteborg, Sweden
| | - Florian David
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Göteborg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Göteborg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Göteborg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, 412 96, Göteborg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
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47
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Swiat MA, Dashko S, den Ridder M, Wijsman M, van der Oost J, Daran JM, Daran-Lapujade P. FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae. Nucleic Acids Res 2017; 45:12585-12598. [PMID: 29106617 PMCID: PMC5716609 DOI: 10.1093/nar/gkx1007] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/13/2017] [Indexed: 11/14/2022] Open
Abstract
Cpf1 is a new class II family of CRISPR-Cas RNA-programmable endonucleases with unique features that make it a very attractive alternative or complement to Cas9 for genome engineering. Using constitutively expressed Cpf1 from Francisella novicida, the present study demonstrates that FnCpf1 can mediate RNA-guided DNA cleavage at targeted genomic loci in the popular model and industrial yeast Saccharomyces cerevisiae. FnCpf1 very efficiently and precisely promoted repair DNA recombination with efficiencies up to 100%. Furthermore, FnCpf1 was shown to introduce point mutations with high fidelity. While editing multiple loci with Cas9 is hampered by the need for multiple or complex expression constructs, processing itself a customized CRISPR array FnCpf1 was able to edit four genes simultaneously in yeast with a 100% efficiency. A remarkable observation was the unexpected, strong preference of FnCpf1 to cleave DNA at target sites harbouring 5′-TTTV-3′ PAM sequences, a motif reported to be favoured by Cpf1 homologs of Acidaminococcus and Lachnospiraceae. The present study supplies several experimentally tested guidelines for crRNA design, as well as plasmids for FnCpf1 expression and easy construction of crRNA expression cassettes in S. cerevisiae. FnCpf1 proves to be a powerful addition to S. cerevisiae CRISPR toolbox.
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Affiliation(s)
- Michal A Swiat
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sofia Dashko
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maxime den Ridder
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Melanie Wijsman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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48
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Besada-Lombana PB, McTaggart TL, Da Silva NA. Molecular tools for pathway engineering in Saccharomyces cerevisiae. Curr Opin Biotechnol 2017; 53:39-49. [PMID: 29274630 DOI: 10.1016/j.copbio.2017.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/26/2022]
Abstract
Molecular tools for the regulation of protein expression in Saccharomyces cerevisiae have contributed to rapid advances in pathway engineering for this yeast. This review considers new and enhanced additions to this toolbox, focusing on experimental approaches to modulate enzyme synthesis and enzyme fate. Methods for genome engineering, regulation of transcription, post-translational protein localization, and combinatorial screening and sensing in S. cerevisiae are highlighted, and promising new approaches are introduced.
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Affiliation(s)
- Pamela B Besada-Lombana
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA
| | - Tami L McTaggart
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA
| | - Nancy A Da Silva
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA.
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