1
|
Sanchez C, Ramirez A, Hodgson L. Unravelling molecular dynamics in living cells: Fluorescent protein biosensors for cell biology. J Microsc 2024. [PMID: 38357769 DOI: 10.1111/jmi.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Genetically encoded, fluorescent protein (FP)-based Förster resonance energy transfer (FRET) biosensors are microscopy imaging tools tailored for the precise monitoring and detection of molecular dynamics within subcellular microenvironments. They are characterised by their ability to provide an outstanding combination of spatial and temporal resolutions in live-cell microscopy. In this review, we begin by tracing back on the historical development of genetically encoded FP labelling for detection in live cells, which lead us to the development of early biosensors and finally to the engineering of single-chain FRET-based biosensors that have become the state-of-the-art today. Ultimately, this review delves into the fundamental principles of FRET and the design strategies underpinning FRET-based biosensors, discusses their diverse applications and addresses the distinct challenges associated with their implementation. We place particular emphasis on single-chain FRET biosensors for the Rho family of guanosine triphosphate hydrolases (GTPases), pointing to their historical role in driving our understanding of the molecular dynamics of this important class of signalling proteins and revealing the intricate relationships and regulatory mechanisms that comprise Rho GTPase biology in living cells.
Collapse
Affiliation(s)
- Colline Sanchez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Andrea Ramirez
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Louis Hodgson
- Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York, USA
| |
Collapse
|
2
|
Gligorovski V, Sadeghi A, Rahi SJ. Multidimensional characterization of inducible promoters and a highly light-sensitive LOV-transcription factor. Nat Commun 2023; 14:3810. [PMID: 37369667 DOI: 10.1038/s41467-023-38959-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The ability to independently control the expression of different genes is important for quantitative biology. Using budding yeast, we characterize GAL1pr, GALL, MET3pr, CUP1pr, PHO5pr, tetOpr, terminator-tetOpr, Z3EV, blue-light inducible optogenetic systems El222-LIP, El222-GLIP, and red-light inducible PhyB-PIF3. We report kinetic parameters, noise scaling, impact on growth, and the fundamental leakiness of each system using an intuitive unit, maxGAL1. We uncover disadvantages of widely used tools, e.g., nonmonotonic activity of MET3pr and GALL, slow off kinetics of the doxycycline- and estradiol-inducible systems tetOpr and Z3EV, and high variability of PHO5pr and red-light activated PhyB-PIF3 system. We introduce two previously uncharacterized systems: strongLOV, a more light-sensitive El222 mutant, and ARG3pr, which is induced in the absence of arginine or presence of methionine. To demonstrate fine control over gene circuits, we experimentally tune the time between cell cycle Start and mitosis, artificially simulating near-wild-type timing. All strains, constructs, code, and data ( https://promoter-benchmark.epfl.ch/ ) are made available.
Collapse
Affiliation(s)
- Vojislav Gligorovski
- Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ahmad Sadeghi
- Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Sahand Jamal Rahi
- Laboratory of the Physics of Biological Systems, Institute of Physics, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| |
Collapse
|
3
|
Zhou LY, Zhang S, Li LY, Yang GY, Zeng L. Optimization of mammalian expression vector by cis-regulatory element combinations. Mol Genet Genomics 2023:10.1007/s00438-023-02042-0. [PMID: 37318628 DOI: 10.1007/s00438-023-02042-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/31/2023] [Indexed: 06/16/2023]
Abstract
The regulation of gene expression in mammalian cells by combining various cis-regulatory features has rarely been discussed. In this study, we constructed expression vectors containing various combinations of regulatory elements to examine the regulation of gene expression by different combinations of cis-regulatory elements. The effects of four promoters (CMV promoter, PGK promoter, Polr2a promoter, and EF-1α core promoter), two enhancers (CMV enhancer and SV40 enhancer), two introns (EF-1α intron A and hybrid intron), two terminators (CYC1 terminator and TEF terminator), and their different combinations on downstream gene expression were compared in various mammalian cells using fluorescence microscopy to observe fluorescence, quantitative real-time PCR (qRT-PCR), and western blot. The receptor binding domain (RBD) sequence from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein was used to replace the eGFP sequence in the expression vector and the RBD expression was detected by qRT-PCR and western blot. The results showed that protein expression can be regulated by optimizing the combination of cis-acting elements. The vector with the CMV enhancer, EF-1α core promoter, and TEF terminator was found to express approximately threefold higher eGFP than the unmodified vector in different animal cells, as well as 2.63-fold higher recombinant RBD protein than the original vector in HEK-293T cells. Moreover, we suggest that combinations of multiple regulatory elements capable of regulating gene expression do not necessarily exhibit synergistic effects to enhance expression further. Overall, our findings provide insights into biological applications that require the regulation of gene expression and will help to optimize expression vectors for biosynthesis and other fields. Additionally, we provide valuable insights into the production of RBD proteins, which may aid in developing reagents for diagnosis and treatment during the COVID-19 pandemic.
Collapse
Affiliation(s)
- Lu-Yu Zhou
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China
| | - Shuang Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China
| | - Li-Yun Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China
| | - Guo-Yu Yang
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China
| | - Lei Zeng
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, People's Republic of China.
- Key Laboratory of Animal Biochemistry and Nutrition, Henan Agricultural University, Ministry of Agriculture and Rural Affairs, Zhengzhou, 450046, Henan, People's Republic of China.
- Key Laboratory of Animal Growth and Development, The Education Department of Henan Province, Zhengzhou, 450046, Henan, People's Republic of China.
| |
Collapse
|
4
|
Durmusoglu D, Al’Abri IS, Collins SP, Cheng J, Eroglu A, Beisel CL, Crook N. In Situ Biomanufacturing of Small Molecules in the Mammalian Gut by Probiotic Saccharomyces boulardii. ACS Synth Biol 2021; 10:1039-1052. [PMID: 33843197 DOI: 10.1021/acssynbio.0c00562] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Saccharomyces boulardii is a probiotic yeast that exhibits rapid growth at 37 °C, is easy to transform, and can produce therapeutic proteins in the gut. To establish its ability to produce small molecules encoded by multigene pathways, we measured the amount and variance in protein expression enabled by promoters, terminators, selective markers, and copy number control elements. We next demonstrated efficient (>95%) CRISPR-mediated genome editing in this strain, allowing us to probe engineered gene expression across different genomic sites. We leveraged these strategies to assemble pathways enabling a wide range of vitamin precursor (β-carotene) and drug (violacein) titers. We found that S. boulardii colonizes germ-free mice stably for over 30 days and competes for niche space with commensal microbes, exhibiting short (1-2 day) gut residence times in conventional and antibiotic-treated mice. Using these tools, we enabled β-carotene synthesis (194 μg total) in the germ-free mouse gut over 14 days, estimating that the total mass of additional β-carotene recovered in feces was 56-fold higher than the β-carotene present in the initial probiotic dose. This work quantifies heterologous small molecule production titers by S. boulardii living in the mammalian gut and provides a set of tools for modulating these titers.
Collapse
Affiliation(s)
- Deniz Durmusoglu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Ibrahim S. Al’Abri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Scott P. Collins
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Junrui Cheng
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Room 3204, Kannapolis, North Carolina 28081, United States
| | - Abdulkerim Eroglu
- Plants for Human Health Institute, North Carolina State University, 600 Laureate Way, Room 3204, Kannapolis, North Carolina 28081, United States
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, 120 Broughton Drive, Room 351, Raleigh, North Carolina 27695-7622, United States
| | - Chase L. Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg 97080, Germany
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| |
Collapse
|
5
|
The activity of yeast Apn2 AP endonuclease at uracil-derived AP sites is dependent on the major carbon source. Curr Genet 2021; 67:283-294. [PMID: 33386486 DOI: 10.1007/s00294-020-01141-4] [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: 09/01/2020] [Revised: 11/16/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
Yeast Apn2 is an AP endonuclease and DNA 3'-diesterase that belongs to the Exo III family with homology to the E. coli exonuclease III, Schizosaccharomyces pombe eth1, and human AP endonucleases APEX1 and APEX2. In the absence of Apn1, the major AP endonuclease in yeast, Apn2 can cleave the DNA backbone at an AP lesion initiating the base excision repair pathway. To study the role and relative contribution of Apn2, we took advantage of a reporter system that was previously used to delineate how uracil-derived AP sites are repaired. At this reporter, disruption of the Apn1-initiated base excision repair pathway led to a significant elevation of A:T to C:G transversions. Here we show that such highly elevated A:T to C:G transversion mutations associated with uracil residues in DNA are abolished when apn1∆ yeast cells are grown in glucose as the primary carbon source. We also show that the disruption of Apn2, either by the complete gene deletion or by the mutation of a catalytic residue, results in a similarly reduced rate of the uracil-associated mutations. Overall, our results indicate that Apn2 activity is regulated by the glucose repression pathway in yeast.
Collapse
|
6
|
De Nijs Y, De Maeseneire SL, Soetaert WK. 5' untranslated regions: the next regulatory sequence in yeast synthetic biology. Biol Rev Camb Philos Soc 2019; 95:517-529. [PMID: 31863552 DOI: 10.1111/brv.12575] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/08/2019] [Accepted: 11/28/2019] [Indexed: 01/10/2023]
Abstract
When developing industrial biotechnology processes, Saccharomyces cerevisiae (baker's yeast or brewer's yeast) is a popular choice as a microbial host. Many tools have been developed in the fields of synthetic biology and metabolic engineering to introduce heterologous pathways and tune their expression in yeast. Such tools mainly focus on controlling transcription, whereas post-transcriptional regulation is often overlooked. Herein we discuss regulatory elements found in the 5' untranslated region (UTR) and their influence on protein synthesis. We provide not only an overall picture, but also a set of design rules on how to engineer a 5' UTR. The reader is also referred to currently available models that allow gene expression to be tuned predictably using different 5' UTRs.
Collapse
Affiliation(s)
- Yatti De Nijs
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Sofie L De Maeseneire
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wim K Soetaert
- Faculty of Bioscience Engineering, Centre for Industrial Biotechnology and Biocatalysis (InBio.be), Department Biotechnology, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| |
Collapse
|
7
|
Liu S, Xiao H, Zhang F, Lu Z, Zhang Y, Deng A, Li Z, Yang C, Wen T. A seamless and iterative DNA assembly method named PS-Brick and its assisted metabolic engineering for threonine and 1-propanol production. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:180. [PMID: 31338122 PMCID: PMC6628500 DOI: 10.1186/s13068-019-1520-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND DNA assembly is an essential technique enabling metabolic engineering and synthetic biology. Combining novel DNA assembly technologies with rational metabolic engineering can facilitate the construction of microbial cell factories. Amino acids and derived biochemicals are important products in industrial biotechnology with wide application and huge markets. DNA assembly scenarios encountered in metabolic engineering for the construction of amino acid and related compound producers, such as design-build-test-learn cycles, construction of precise genetic circuits and repetitive DNA molecules, usually require for iterative, scarless and repetitive sequence assembly methods, respectively. RESULTS Restriction endonuclease (RE)-assisted strategies constitute one of the major categories of DNA assembly. Here, we developed a Type IIP and IIS RE-assisted method named PS-Brick that comprehensively takes advantage of the properties of PCR fragments and REs for iterative, seamless and repetitive sequence assembly. One round of PS-Brick reaction using purified plasmids and PCR fragments was accomplished within several hours, and transformation of the resultant reaction product from this PS-Brick assembly reaction exhibited high efficiency (104-105 CFUs/µg DNA) and high accuracy (~ 90%). An application of metabolic engineering to threonine production, including the release of feedback regulation, elimination of metabolic bottlenecks, intensification of threonine export and inactivation of threonine catabolism, was stepwise resolved in E. coli by rounds of "design-build-test-learn" cycles through the iterative PS-Brick paradigm, and 45.71 g/L threonine was obtained through fed-batch fermentation. In addition to the value of the iterative character of PS-Brick for sequential strain engineering, seamless cloning enabled precise in-frame fusion for codon saturation mutagenesis and bicistronic design, and the repetitive sequence cloning ability of PS-Brick enabled construction of tandem CRISPR sgRNA arrays for genome editing. Moreover, the heterologous pathway deriving 1-propanol pathway from threonine, composed of Lactococcus lactis kivD and Saccharomyces cerevisiae ADH2, was assembled by one cycle of PS-Brick, resulting in 1.35 g/L 1-propanol in fed-batch fermentation. CONCLUSIONS To the best of our knowledge, the PS-Brick framework is the first RE-assisted DNA assembly method using the strengths of both Type IIP and IIS REs. In this study, PS-Brick was demonstrated to be an efficient DNA assembly method for pathway construction and genome editing and was successfully applied in design-build-test-learn (DBTL) cycles of metabolic engineering for the production of threonine and threonine-derived 1-propanol. The PS-Brick presents a valuable addition to the current toolbox of synthetic biology and metabolic engineering.
Collapse
Affiliation(s)
- Shuwen Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Haihan Xiao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fangfang Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230039 China
| | - Zheng Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yun Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Aihua Deng
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhongcai Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Cui Yang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Tingyi Wen
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 100049 China
| |
Collapse
|
8
|
Presnell KV, Flexer-Harrison M, Alper HS. Design and synthesis of synthetic UP elements for modulation of gene expression in Escherichia coli. Synth Syst Biotechnol 2019; 4:99-106. [PMID: 31080900 PMCID: PMC6501063 DOI: 10.1016/j.synbio.2019.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/10/2019] [Accepted: 04/11/2019] [Indexed: 11/29/2022] Open
Abstract
Metabolic engineering requires fine-tuned gene expression for most pathway optimization applications. To develop a suitable suite of promoters, traditional bacterial promoter engineering efforts have focused on modifications to the core region, especially the −10 and −35 regions, of native promoters. Here, we demonstrate an alternate, unexplored route of promoter engineering through randomization of the UP element of the promoter—a region that contacts the alpha subunit carboxy-terminal domain instead of the sigma subunit of the RNA polymerase holoenzyme. Through this work, we identify five novel UP element sequences through library-based searches in Escherichia coli. The resulting elements were used to activate the E. coli core promoter, rrnD promoter, to levels on par and higher than the prevalent strong bacterial promoter, OXB15. These relative levels of expression activation were transferrable when applied upstream of alternate core promoter sequences, including rrnA and rrnH. This work thus presents and validates a novel strategy for bacterial promoter engineering with transferability across varying core promoters and potential for transferability across bacterial species.
Collapse
Affiliation(s)
- Kristin V Presnell
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Madeleine Flexer-Harrison
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX, 78712, USA
| |
Collapse
|
9
|
Weenink T, van der Hilst J, McKiernan RM, Ellis T. Design of RNA hairpin modules that predictably tune translation in yeast. Synth Biol (Oxf) 2018; 3:ysy019. [PMID: 32995525 PMCID: PMC7445769 DOI: 10.1093/synbio/ysy019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Modular parts for tuning translation are prevalent in prokaryotic synthetic biology but lacking for eukaryotic synthetic biology. Working in Saccharomyces cerevisiae yeast, we here describe how hairpin RNA structures inserted into the 5′ untranslated region (5′UTR) of mRNAs can be used to tune expression levels by 100-fold by inhibiting translation. We determine the relationship between the calculated free energy of folding in the 5′UTR and in vivo protein abundance, and show that this enables rational design of hairpin libraries that give predicted expression outputs. Our approach is modular, working with different promoters and protein coding sequences, and outperforms promoter mutation as a way to predictably generate a library where a protein is induced to express at a range of different levels. With this new tool, computational RNA sequence design can be used to predictably fine-tune protein production for genes expressed in yeast.
Collapse
Affiliation(s)
- Tim Weenink
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Jelle van der Hilst
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Robert M McKiernan
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | - Tom Ellis
- Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK.,Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| |
Collapse
|
10
|
Decoene T, Peters G, De Maeseneire SL, De Mey M. Toward Predictable 5'UTRs in Saccharomyces cerevisiae: Development of a yUTR Calculator. ACS Synth Biol 2018; 7:622-634. [PMID: 29366325 DOI: 10.1021/acssynbio.7b00366] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fine-tuning biosynthetic pathways is crucial for the development of economic feasible microbial cell factories. Therefore, the use of computational models able to predictably design regulatory sequences for pathway engineering proves to be a valuable tool, especially for modifying genes at the translational level. In this study we developed a computational approach for the de novo design of 5'-untranslated regions (5'UTRs) in Saccharomyces cerevisiae with a predictive outcome on translation initiation rate. On the basis of existing data, a partial least-squares (PLS) regression model was trained and showed good performance on predicting protein abundances of an independent test set. This model was further used for the construction of a "yUTR calculator" that can design 5'UTR sequences with a diverse range of desired translation efficiencies. The predictive power of our yUTR calculator was confirmed in vivo by different representative case studies. As such, these results show the great potential of data driven approaches for reliable pathway engineering in S. cerevisiae.
Collapse
Affiliation(s)
- Thomas Decoene
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Gert Peters
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Sofie L. De Maeseneire
- Centre
for Industrial Biotechnology and Biocatalysis, Ghent University, Coupure
links 653, 9000 Ghent, Belgium
| | - Marjan De Mey
- Centre
for Synthetic Biology, Ghent University, Coupure links 653, 9000 Ghent, Belgium
| |
Collapse
|
11
|
Combinatorial pathway optimization for streamlined metabolic engineering. Curr Opin Biotechnol 2017; 47:142-151. [DOI: 10.1016/j.copbio.2017.06.014] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/19/2017] [Indexed: 11/20/2022]
|
12
|
Deaner M, Alper HS. Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae. Metab Eng 2017; 40:14-22. [DOI: 10.1016/j.ymben.2017.01.012] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 12/22/2022]
|
13
|
Sun J, Alper H. Synthetic Biology: An Emerging Approach for Strain Engineering. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Jie Sun
- Department of Chemical Engineering; The University of Texas at Austin; 200 E Dean Keeton Street Stop C0400, Austin TX 78712 USA
| | - Hal Alper
- Department of Chemical Engineering; The University of Texas at Austin; 200 E Dean Keeton Street Stop C0400, Austin TX 78712 USA
| |
Collapse
|
14
|
Gan R, Jewett MC. Evolution of translation initiation sequences using in vitro yeast ribosome display. Biotechnol Bioeng 2016; 113:1777-86. [PMID: 26757179 DOI: 10.1002/bit.25933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 12/13/2015] [Accepted: 01/07/2016] [Indexed: 11/08/2022]
Abstract
We report a novel in vitro yeast ribosome display method based on cell-free protein synthesis (CFPS) using linear DNA templates. We demonstrate that our platform can enrich a target gene from a model library by 100-fold per round of selection. We demonstrate the utility of our approach by evolving cap-independent translation initiation (CITI) sequences, which result in a 13-fold increase in CFPS yields after four rounds of selection, and a threefold further increase by placing the beneficial short sequences in tandem. We also show that 12 of the selected CITI sequences permit precise control of gene expression in vitro over a range of up to 80-fold by enhancing translation (and not as cryptic promoters). These 12 sequences are then shown to tune protein expression in vivo, though likely due to a different mechanism. Looking forward, yeast ribosome display holds promise for evolving libraries of proteins and DNA regulatory parts for protein engineering and synthetic biology. Biotechnol. Bioeng. 2016;113: 1777-1786. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Rui Gan
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois. .,Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois. .,Simpson Querrey Institute, Northwestern University, Evanston, Illinois.
| |
Collapse
|
15
|
|
16
|
Leavitt JM, Alper HS. Advances and current limitations in transcript-level control of gene expression. Curr Opin Biotechnol 2015; 34:98-104. [DOI: 10.1016/j.copbio.2014.12.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/14/2014] [Accepted: 12/15/2014] [Indexed: 11/25/2022]
|
17
|
Vogl T, Ahmad M, Krainer FW, Schwab H, Glieder A. Restriction site free cloning (RSFC) plasmid family for seamless, sequence independent cloning in Pichia pastoris. Microb Cell Fact 2015; 14:103. [PMID: 26169367 PMCID: PMC4501187 DOI: 10.1186/s12934-015-0293-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/30/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Tagging proteins is a standard method facilitating protein detection, purification or targeting. When tagging a certain protein of interest, it is challenging to predict which tag will give optimal results and will not interfere with protein folding, activity or yields. Ideally, multiple tags and positions are tested which however complicates molecular cloning and expression vector generation. In conventional cloning, tags are either added on PCR primers (requiring a distinct primer and PCR product per tag) or provided on the vector (typically leaving a restriction site scar). RESULTS Here we report a vector family of 40 plasmids allowing simple, seamless fusions of a single PCR product with various N- and C-terminal tags, signal sequences and promoters. The restriction site free cloning (RSFC) strategy presented in this paper relies on seamless cloning using type IIS restriction endonucleases. After cutting out a stuffer (placeholder) fragment from the vectors, a single PCR product can be directly inserted in frame into all 40 plasmids using blunt end or TA ligations, requiring only verification of the orientation. We have established a RSFC vector family for the commonly used protein expression host Pichia pastoris and demonstrated the system with the secretory expression of horseradish peroxidase (HRP). HRP fusions to four tags (Myc, FLAG, His, Strep) and two fusion proteins (GFP and MBP) showed a 31-fold difference in volumetric activities. C-terminal tagging caused in some cases almost a complete loss of function, whereas N-terminal tags showed moderate differences. CONCLUSIONS The RSFC vectors provide an unprecedented toolbox for expression optimization in P. pastoris. The results obtained with HRP underline the importance of comparing different tags to maximize activities of fusion proteins. In a similar fashion the RSFC strategy can be applied in other expression hosts to screen for optimal promoters, signal sequences or to facilitate the evaluation of (iso-) enzyme families.
Collapse
Affiliation(s)
- Thomas Vogl
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria. .,Queensland University of Technology, 2 George St., Brisbane, QLD, 4000, Australia.
| | - Mudassar Ahmad
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Florian W Krainer
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Helmut Schwab
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| | - Anton Glieder
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.
| |
Collapse
|
18
|
Casini A, Storch M, Baldwin GS, Ellis T. Bricks and blueprints: methods and standards for DNA assembly. Nat Rev Mol Cell Biol 2015; 16:568-76. [DOI: 10.1038/nrm4014] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
19
|
Functional optimization of gene clusters by combinatorial design and assembly. Nat Biotechnol 2014; 32:1241-9. [PMID: 25419741 DOI: 10.1038/nbt.3063] [Citation(s) in RCA: 251] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 10/07/2014] [Indexed: 01/21/2023]
Abstract
Large microbial gene clusters encode useful functions, including energy utilization and natural product biosynthesis, but genetic manipulation of such systems is slow, difficult and complicated by complex regulation. We exploit the modularity of a refactored Klebsiella oxytoca nitrogen fixation (nif) gene cluster (16 genes, 103 parts) to build genetic permutations that could not be achieved by starting from the wild-type cluster. Constraint-based combinatorial design and DNA assembly are used to build libraries of radically different cluster architectures by varying part choice, gene order, gene orientation and operon occupancy. We construct 84 variants of the nifUSVWZM operon, 145 variants of the nifHDKY operon, 155 variants of the nifHDKYENJ operon and 122 variants of the complete 16-gene pathway. The performance and behavior of these variants are characterized by nitrogenase assay and strand-specific RNA sequencing (RNA-seq), and the results are incorporated into subsequent design cycles. We have produced a fully synthetic cluster that recovers 57% of wild-type activity. Our approach allows the performance of genetic parts to be quantified simultaneously in hundreds of genetic contexts. This parallelized design-build-test-learn cycle, which can access previously unattainable regions of genetic space, should provide a useful, fast tool for genetic optimization and hypothesis testing.
Collapse
|
20
|
Redden H, Morse N, Alper HS. The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Res 2014; 15:1-10. [DOI: 10.1111/1567-1364.12188] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/28/2014] [Accepted: 07/15/2014] [Indexed: 02/04/2023] Open
Affiliation(s)
- Heidi Redden
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
| | - Nicholas Morse
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
| | - Hal S. Alper
- Department for Molecular Biosciences; The University of Texas at Austin; Austin TX USA
- McKetta Department of Chemical Engineering; The University of Texas at Austin; Austin TX USA
| |
Collapse
|
21
|
Design of synthetic yeast promoters via tuning of nucleosome architecture. Nat Commun 2014; 5:4002. [PMID: 24862902 PMCID: PMC4064463 DOI: 10.1038/ncomms5002] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/29/2014] [Indexed: 11/29/2022] Open
Abstract
Model-based design of biological parts is a critical goal of synthetic biology, especially for eukaryotes. Here we demonstrate that nucleosome architecture can play a role in defining yeast promoter activity and utilize a computationally-guided approach that can enable both the redesign of endogenous promoter sequences and the de novo design of synthetic promoters. Initially, we use our approach to reprogram native promoters for increased expression and evaluate their performance in various genetic contexts. Increases in expression ranging from 1.5 to nearly 6-fold in a plasmid-based system and up to 16-fold in a genomic context were obtained. Next, we demonstrate that, in a single design cycle, it is possible to create functional, purely synthetic yeast promoters that achieve substantial expression levels (within the top sixth percentile among native yeast promoters). In doing so, this work establishes a unique DNA-level specification of promoter activity and demonstrates predictive design of synthetic parts.
Collapse
|
22
|
|
23
|
Casini A, MacDonald JT, De Jonghe J, Christodoulou G, Freemont PS, Baldwin GS, Ellis T. One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy. Nucleic Acids Res 2013; 42:e7. [PMID: 24153110 PMCID: PMC3874208 DOI: 10.1093/nar/gkt915] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Overlap-directed DNA assembly methods allow multiple DNA parts to be assembled together in one reaction. These methods, which rely on sequence homology between the ends of DNA parts, have become widely adopted in synthetic biology, despite being incompatible with a key principle of engineering: modularity. To answer this, we present MODAL: a Modular Overlap-Directed Assembly with Linkers strategy that brings modularity to overlap-directed methods, allowing assembly of an initial set of DNA parts into a variety of arrangements in one-pot reactions. MODAL is accompanied by a custom software tool that designs overlap linkers to guide assembly, allowing parts to be assembled in any specified order and orientation. The in silico design of synthetic orthogonal overlapping junctions allows for much greater efficiency in DNA assembly for a variety of different methods compared with using non-designed sequence. In tests with three different assembly technologies, the MODAL strategy gives assembly of both yeast and bacterial plasmids, composed of up to five DNA parts in the kilobase range with efficiencies of between 75 and 100%. It also seamlessly allows mutagenesis to be performed on any specified DNA parts during the process, allowing the one-step creation of construct libraries valuable for synthetic biology applications.
Collapse
Affiliation(s)
- Arturo Casini
- Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK and Department of Bioengineering, Imperial College London, London SW7 2AZ, UK
| | | | | | | | | | | | | |
Collapse
|
24
|
Lamping E, Niimi M, Cannon RD. Small, synthetic, GC-rich mRNA stem-loop modules 5' proximal to the AUG start-codon predictably tune gene expression in yeast. Microb Cell Fact 2013; 12:74. [PMID: 23895661 PMCID: PMC3765126 DOI: 10.1186/1475-2859-12-74] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 07/10/2013] [Indexed: 12/03/2022] Open
Abstract
Background A large range of genetic tools has been developed for the optimal design and regulation of complex metabolic pathways in bacteria. However, fewer tools exist in yeast that can precisely tune the expression of individual enzymes in novel metabolic pathways suitable for industrial-scale production of non-natural compounds. Tuning expression levels is critical for reducing the metabolic burden of over-expressed proteins, the accumulation of toxic intermediates, and for redirecting metabolic flux from native pathways involving essential enzymes without negatively affecting the viability of the host. We have developed a yeast membrane protein hyper-expression system with critical advantages over conventional, plasmid-based, expression systems. However, expression levels are sometimes so high that they adversely affect protein targeting/folding or the growth and/or phenotype of the host. Here we describe the use of small synthetic mRNA control modules that allowed us to predictably tune protein expression levels to any desired level. Down-regulation of expression was achieved by engineering small GC-rich mRNA stem-loops into the 5′ UTR that inhibited translation initiation of the yeast ribosomal 43S preinitiation complex (PIC). Results Exploiting the fact that the yeast 43S PIC has great difficulty scanning through GC-rich mRNA stem-loops, we created yeast strains containing 17 different RNA stem-loop modules in the 5′ UTR that expressed varying amounts of the fungal multidrug efflux pump reporter Cdr1p from Candida albicans. Increasing the length of mRNA stem-loops (that contained only GC-pairs) near the AUG start-codon led to a surprisingly large decrease in Cdr1p expression; ~2.7-fold for every additional GC-pair added to the stem, while the mRNA levels remained largely unaffected. An mRNA stem-loop of seven GC-pairs (∆G = −15.8 kcal/mol) reduced Cdr1p expression levels by >99%, and even the smallest possible stem-loop of only three GC-pairs (∆G = −4.4 kcal/mol) inhibited Cdr1p expression by ~50%. Conclusion We have developed a simple cloning strategy to fine-tune protein expression levels in yeast that has many potential applications in metabolic engineering and the optimization of protein expression in yeast. This study also highlights the importance of considering the use of multiple cloning-sites carefully to preclude unwanted effects on gene expression.
Collapse
Affiliation(s)
- Erwin Lamping
- Sir John Walsh Research Institute, University of Otago, Dunedin 9054, New Zealand.
| | | | | |
Collapse
|
25
|
Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications. Metab Eng 2013; 19:88-97. [PMID: 23856240 DOI: 10.1016/j.ymben.2013.07.001] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/12/2013] [Accepted: 07/03/2013] [Indexed: 01/24/2023]
Abstract
Control of gene and protein expression of both endogenous and heterologous genes is a key component of metabolic engineering. While a large amount of work has been published characterizing promoters for this purpose, less effort has been exerted to elucidate the role of terminators in yeast. In this study, we characterize over 30 terminators for use in metabolic engineering applications in Saccharomyces cerevisiae and determine mRNA half-life changes to be the major cause of the varied protein and transcript expression level. We demonstrate that the difference in transcript level can be over 6.5-fold even for high strength promoters. The influence of terminator selection is magnified when coupled with a low-expression promoter, with a maximum difference in protein expression of 11-fold between an expression-enhancing terminator and the parent plasmid terminator and over 35-fold difference when compared with a no-terminator baseline. This is the first time that terminators have been investigated in the context of multiple promoters spanning orders of magnitude in activity. Finally, we demonstrate the utility of terminator selection for metabolic engineering by using a mutant xylose isomerase gene as a proof-of-concept. Through pairing an expression-enhancing terminator with a low-expression promoter, we were able to achieve the same phenotypic result as with a promoter considerably higher in strength. Moreover, we can further boost the phenotype of the high-strength promoter by pairing it with an expression-enhancing terminator. This work highlights how terminator elements can be used to control metabolic pathways in the same way that promoters are traditionally used in yeast. Together, this work demonstrates that terminators will be an important part of heterologous gene expression and metabolic engineering for yeast in the future.
Collapse
|
26
|
Karim AS, Curran KA, Alper HS. Characterization of plasmid burden and copy number in Saccharomyces cerevisiae for optimization of metabolic engineering applications. FEMS Yeast Res 2012; 13:107-16. [PMID: 23107142 DOI: 10.1111/1567-1364.12016] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 10/22/2012] [Accepted: 10/23/2012] [Indexed: 11/28/2022] Open
Abstract
Many metabolic engineering and genetic engineering applications in yeast rely on the use of plasmids. Despite their pervasive use and the diverse collections available, there is a fundamental lack of understanding of how commonly used DNA plasmids affect the cell's ability to grow and how the choice of plasmid components can influence plasmid load and burden. In this study, we characterized the major attributes of the 2 micron and centromeric plasmids typically used in yeast by examining the impact of choice of selection marker, promoter, origin of replication, and strain ploidy on conferred growth rates and plasmid copy number. We conclude that the 'plasmid burden', as demonstrated by a reduced growth rate, is primarily due to the choice of selection marker, especially when auxotrophic markers are utilized. The plasmid burden traditionally attributed to replication and maintenance of plasmid DNA plays only a minor role in haploid yeast yet is much more significant in diploid strains. The selection marker can also significantly change plasmid copy number. In fact, plasmid copy number can be influenced to some extent by all of the parameters tested. The information presented in this study will allow for more rational design and selection of plasmids for engineering applications.
Collapse
Affiliation(s)
- Ashty S Karim
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | | | | |
Collapse
|
27
|
Miklos AE, Hughes RA, Ellington AD. Design and assembly of large synthetic DNA constructs. ACTA ACUST UNITED AC 2012; Chapter 3:Unit3.23. [PMID: 22870858 DOI: 10.1002/0471142727.mb0323s99] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The availability of custom synthetic gene-length DNA products removes numerous bottlenecks in research efforts, making gene synthesis an increasingly common commercial service. However, the assembly of synthetic oligonucleotides into large, custom DNA constructs is not especially difficult, and performing "in-house" gene synthesis has time and cost advantages. This unit will treat both the concerns of design and physical assembly in gene synthesis, including how to design DNA sequences for synthesis and the design of overlapping oligonucleotide schemes to ensure facile assembly into the final product. Assembly is accomplished using a reliable series of PCR reactions, with a troubleshooting assembly protocol included, which not only assembles difficult sequences but allows identification of the source of a failure down to a pair of oligonucleotides.
Collapse
Affiliation(s)
- Aleksandr E Miklos
- The University of Texas at Austin, Applied Research Laboratories, Department of Chemistry and Biochemistry, Center for Systems and Synthetic Biology, Austin, Texas, USA
| | | | | |
Collapse
|
28
|
Blazeck J, Alper HS. Promoter engineering: Recent advances in controlling transcription at the most fundamental level. Biotechnol J 2012; 8:46-58. [DOI: 10.1002/biot.201200120] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/25/2012] [Accepted: 07/17/2012] [Indexed: 12/25/2022]
|
29
|
Xu P, Vansiri A, Bhan N, Koffas MAG. ePathBrick: a synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synth Biol 2012; 1:256-66. [PMID: 23651248 DOI: 10.1021/sb300016b] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Harnessing cell factories for producing biofuel and pharmaceutical molecules has stimulated efforts to develop novel synthetic biology tools customized for modular pathway engineering and optimization. Here we report the development of a set of vectors compatible with BioBrick standards and its application in metabolic engineering. The engineered ePathBrick vectors comprise four compatible restriction enzyme sites allocated on strategic positions so that different regulatory control signals can be reused and manipulation of expression cassette can be streamlined. Specifically, these vectors allow for fine-tuning gene expression by integrating multiple transcriptional activation or repression signals into the operator region. At the same time, ePathBrick vectors support the modular assembly of pathway components and combinatorial generation of pathway diversities with three distinct configurations. We also demonstrated the functionality of a seven-gene pathway (~9 Kb) assembled on one single ePathBrick vector. The ePathBrick vectors presented here provide a versatile platform for rapid design and optimization of metabolic pathways in E. coli.
Collapse
Affiliation(s)
- Peng Xu
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Amerin Vansiri
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Namita Bhan
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Mattheos A. G. Koffas
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| |
Collapse
|
30
|
Blount BA, Weenink T, Ellis T. Construction of synthetic regulatory networks in yeast. FEBS Lett 2012; 586:2112-21. [DOI: 10.1016/j.febslet.2012.01.053] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 01/25/2012] [Accepted: 01/26/2012] [Indexed: 11/30/2022]
|
31
|
Da Silva NA, Srikrishnan S. Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae. FEMS Yeast Res 2012; 12:197-214. [PMID: 22129153 DOI: 10.1111/j.1567-1364.2011.00769.x] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Revised: 11/23/2011] [Accepted: 11/23/2011] [Indexed: 11/26/2022] Open
Abstract
Metabolic pathway engineering in the yeast Saccharomyces cerevisiae leads to improved production of a wide range of compounds, ranging from ethanol (from biomass) to natural products such as sesquiterpenes. The introduction of multienzyme pathways requires precise control over the level and timing of expression of the associated genes. Gene number and promoter strength/regulation are two critical control points, and multiple studies have focused on modulating these in yeast. This MiniReview focuses on methods for introducing genes and controlling their copy number and on the many promoters (both constitutive and inducible) that have been successfully employed. The advantages and disadvantages of the methods will be presented, and applications to pathway engineering will be highlighted.
Collapse
Affiliation(s)
- Nancy A Da Silva
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA.
| | | |
Collapse
|