1
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Jin Z, Vighi A, Dong Y, Bureau JA, Ignea C. Engineering membrane architecture for biotechnological applications. Biotechnol Adv 2023; 64:108118. [PMID: 36773706 DOI: 10.1016/j.biotechadv.2023.108118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Cellular membranes, predominantly described as a dynamic bilayer, are composed of different lipids, transmembrane proteins, and carbohydrates. Most research on biological membranes focuses on the identification, characterization, and mechanistic aspects of their different components. These studies provide a fundamental understanding of membrane structure, function, and dynamics, establishing a basis for the development of membrane engineering strategies. To date, approaches in this field concentrate on membrane adaptation to harsh conditions during industrial fermentation, which can be caused by temperature, osmotic, or organic solvent stress. With advances in the field of metabolic engineering and synthetic biology, recent breakthroughs include proof of concept microbial production of essential medicines, such as cannabinoids and vinblastine. However, long pathways, low yields, and host adaptation continue to pose challenges to the efficient scale up production of many important compounds. The lipid bilayer is profoundly linked to the activity of heterologous membrane-bound enzymes and transport of metabolites. Therefore, strategies for improving enzyme performance, facilitating pathway reconstruction, and enabling storage of products to increase the yields directly involve cellular membranes. At the forefront of membrane engineering research are re-emerging approaches in lipid research and synthetic biology that manipulate membrane size and composition and target lipid profiles across species. This review summarizes engineering strategies applied to cellular membranes and discusses the challenges and future perspectives, particularly with regards to their applications in host engineering and bioproduction.
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Affiliation(s)
- Zimo Jin
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Asia Vighi
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | | | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada.
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2
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He S, Zhang Z, Lu W. Natural promoters and promoter engineering strategies for metabolic regulation in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2023; 50:6986260. [PMID: 36633543 PMCID: PMC9936215 DOI: 10.1093/jimb/kuac029] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023]
Abstract
Sharomyces cerevisiae is currently one of the most important foreign gene expression systems. S. cerevisiae is an excellent host for high-value metabolite cell factories due to its advantages of simplicity, safety, and nontoxicity. A promoter, as one of the basic elements of gene transcription, plays an important role in regulating gene expression and optimizing metabolic pathways. Promoters control the direction and intensity of transcription, and the application of promoters with different intensities and performances will largely determine the effect of gene expression and ultimately affect the experimental results. Due to its significant role, there have been many studies on promoters for decades. While some studies have explored and analyzed new promoters with different functions, more studies have focused on artificially modifying promoters to meet their own scientific needs. Thus, this article reviews current research on promoter engineering techniques and related natural promoters in S. cerevisiae. First, we introduce the basic structure of promoters and the classification of natural promoters. Then, the classification of various promoter strategies is reviewed. Finally, by grouping related articles together using various strategies, this review anticipates the future development direction of promoter engineering.
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Affiliation(s)
| | - Zhanwei Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China
| | - Wenyu Lu
- Correspondence should be addressed to: W. Y. Lu, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, PR China. Phone: +86-22-853-56523. Fax: +86-22-274-00973. E-mail:
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3
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Sanford A, Kiriakov S, Khalil AS. A Toolkit for Precise, Multigene Control in Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:3912-3920. [PMID: 36367334 PMCID: PMC9764411 DOI: 10.1021/acssynbio.2c00423] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Systems that allow researchers to precisely control the expression of genes are fundamental to biological research, biotechnology, and synthetic biology. However, few inducible gene expression systems exist that can enable simultaneous multigene control under common nutritionally favorable conditions in the important model organism and chassis Saccharomyces cerevisiae. Here we repurposed ligand binding domains from mammalian type I nuclear receptors to establish a family of up to five orthogonal synthetic gene expression systems in yeast. Our systems enable tight, independent, multigene control through addition of inert hormones and are capable of driving robust and rapid gene expression outputs, in some cases achieving up to 600-fold induction. As a proof of principle, we placed expression of four enzymes from the violacein biosynthetic pathway under independent expression control to selectively route pathway flux by addition of specific inducer combinations. Our results establish a modular, versatile, and potentially expandable toolkit for multidimensional control of gene expression in yeast that can be used to construct and control naturally occurring and synthetic gene networks.
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Affiliation(s)
- Adam Sanford
- Biological
Design Center, Boston University, Boston, Massachusetts 02215, United States,Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Szilvia Kiriakov
- Biological
Design Center, Boston University, Boston, Massachusetts 02215, United States,Program
in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Ahmad S. Khalil
- Biological
Design Center, Boston University, Boston, Massachusetts 02215, United States,Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States,Program
in Molecular Biology, Cell Biology, and Biochemistry, Boston University, Boston, Massachusetts 02215, United States,Wyss
Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, United States,
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4
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Schrevens S, Sanglard D. A novel Candida glabrata doxycycline-inducible system for in vitro/in vivo use. FEMS Yeast Res 2022; 22:6680246. [PMID: 36047937 PMCID: PMC9508828 DOI: 10.1093/femsyr/foac046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
Candida glabrata is an important pathogen causing superficial to invasive disease in human. Conditional expression systems are helpful in addressing the function of genes and especially when they can be applied to in vivo studies. Tetracycline-dependent regulation systems have been used in diverse fungi to turn-on (Tet-on) or turn-off (Tet-off) gene expression either in vitro but also in vivo in animal models. Up to now, only a Tet-off expression has been constructed for gene expression in C. glabrata. Here, we report a Tet-on gene expression system which can be used in vitro and in vivo in any C. glabrata genetic background. This system was used in a mice model of systemic infection to demonstrate that the general amino acid permease Gap1 is important for C. glabrata virulence.
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Affiliation(s)
- S Schrevens
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
| | - D Sanglard
- Institute of Microbiology, University of Lausanne and University Hospital, CH-1011 Lausanne, Switzerland
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5
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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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6
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Cazier AP, Blazeck J. Advances in promoter engineering: novel applications and predefined transcriptional control. Biotechnol J 2021; 16:e2100239. [PMID: 34351706 DOI: 10.1002/biot.202100239] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Synthetic biology continues to progress by relying on more robust tools for transcriptional control, of which promoters are the most fundamental component. Numerous studies have sought to characterize promoter function, determine principles to guide their engineering, and create promoters with stronger expression or tailored inducible control. In this review, we will summarize promoter architecture and highlight recent advances in the field, focusing on the novel applications of inducible promoter design and engineering towards metabolic engineering and cellular therapeutic development. Additionally, we will highlight how the expansion of new, machine learning techniques for modeling and engineering promoter sequences are enabling more accurate prediction of promoter characteristics. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andrew P Cazier
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
| | - John Blazeck
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
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7
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Moore WM, Milshteyn D, Tsai YT, Budin I. Engineering the bilayer: Emerging genetic tool kits for mechanistic lipid biology. Curr Opin Chem Biol 2021; 65:66-73. [PMID: 34218059 DOI: 10.1016/j.cbpa.2021.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 11/19/2022]
Abstract
The structural diversity of lipids underpins the biophysical properties of cellular membranes, which vary across all scales of biological organization. Because lipid composition results from complex metabolic and transport pathways, its experimental control has been a major goal of mechanistic membrane biology. Here, we argue that in the wake of synthetic biology, similar metabolic engineering strategies can be applied to control the composition, physicochemical properties, and function of cell membranes. In one emerging area, titratable expression platforms allow for specific and genome-wide alterations in lipid biosynthetic genes, providing analog control over lipidome stoichiometry in membranes. Simultaneously, heterologous expression of biosynthetic genes and pathways has allowed for gain-of-function experiments with diverse lipids in non-native systems. Finally, we highlight future directions for tool development, including recently discovered lipid transport pathways to intracellular lipid pools. Further tool development providing synthetic control of membrane properties can allow biologists to untangle membrane lipid structure-associated functions.
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Affiliation(s)
- William M Moore
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Daniel Milshteyn
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Yi-Ting Tsai
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Itay Budin
- Department of Chemistry & Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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8
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Saccharomyces cerevisiae Promoter Engineering before and during the Synthetic Biology Era. BIOLOGY 2021; 10:biology10060504. [PMID: 34204069 PMCID: PMC8229000 DOI: 10.3390/biology10060504] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/04/2021] [Accepted: 06/04/2021] [Indexed: 11/19/2022]
Abstract
Simple Summary Promoters are DNA sequences where the process of transcription starts. They can work constitutively or be controlled by environmental signals of different types. The quantity of proteins and RNA present in yeast genetic circuits highly depends on promoter strength. Hence, they have been deeply studied and modified over, at least, the last forty years, especially since the year 2000 when Synthetic Biology was born. Here, we present how promoter engineering changed over these four decades and discuss its possible future directions due to novel computational methods and technology. Abstract Synthetic gene circuits are made of DNA sequences, referred to as transcription units, that communicate by exchanging proteins or RNA molecules. Proteins are, mostly, transcription factors that bind promoter sequences to modulate the expression of other molecules. Promoters are, therefore, key components in genetic circuits. In this review, we focus our attention on the construction of artificial promoters for the yeast S. cerevisiae, a popular chassis for gene circuits. We describe the initial techniques and achievements in promoter engineering that predated the start of the Synthetic Biology epoch of about 20 years. We present the main applications of synthetic promoters built via different methods and discuss the latest innovations in the wet-lab engineering of novel promoter sequences.
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9
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Du Y, Yang B, Yi Z, Hu L, Li M. Engineering Saccharomyces cerevisiae Coculture Platform for the Production of Flavonoids. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:2146-2154. [PMID: 31984739 DOI: 10.1021/acs.jafc.9b07916] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Flavonoids are valuable natural products widely used in human health and nutrition applications. Engineering microbial consortia to express complex flavonoid biosynthetic pathways is a promising approach for flavonoid production. In this study, the entire flavonoid biosynthetic pathway was split into two independent pathways, each of which was contained in separate Saccharomyces cerevisiae cells. The first cell type, sNAR5, which was genetically engineered to express the naringenin biosynthetic pathway, produced 144.1 mg/L naringenin. The second cell type was genetically modified with the heterologous naringenin-to-delphinidin pathway. A coculture produced a delphinidin titer, significantly higher than that produced in a monoculture of strain sDPD2, harboring the entire pathway. Furthermore, we successfully employed this coculture platform for the production of 3 flavonols and 2 anthocyanidins in flask-scale culture. This coculture platform paves the way for the development of an economical and efficient process for microbial flavonoid production.
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Affiliation(s)
- Yun Du
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China
| | - Binrui Yang
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China
| | - Zhiqiang Yi
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China
| | - Lanlan Hu
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China
| | - Mu Li
- Hubei International Scientific and Technological Cooperation Base of Traditional Fermented Foods, Key Laboratory of Environment Correlative Dietology, College of Food Science and Technology , Huazhong Agricultural University , Wuhan , Hubei Province 430070 , China
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10
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Zhou W, Dorrity MW, Bubb KL, Queitsch C, Fields S. Binding and Regulation of Transcription by Yeast Ste12 Variants To Drive Mating and Invasion Phenotypes. Genetics 2020; 214:397-407. [PMID: 31810988 PMCID: PMC7017024 DOI: 10.1534/genetics.119.302929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/25/2019] [Indexed: 12/31/2022] Open
Abstract
Amino acid substitutions are commonly found in human transcription factors, yet the functional consequences of much of this variation remain unknown, even in well-characterized DNA-binding domains. Here, we examine how six single-amino acid variants in the DNA-binding domain of Ste12-a yeast transcription factor regulating mating and invasion-alter Ste12 genome binding, motif recognition, and gene expression to yield markedly different phenotypes. Using a combination of the "calling-card" method, RNA sequencing, and HT-SELEX (high throughput systematic evolution of ligands by exponential enrichment), we find that variants with dissimilar binding and expression profiles can converge onto similar cellular behaviors. Mating-defective variants led to decreased expression of distinct subsets of genes necessary for mating. Hyper-invasive variants also decreased expression of subsets of genes involved in mating, but increased the expression of other subsets of genes associated with the cellular response to osmotic stress. While single-amino acid changes in the coding region of this transcription factor result in complex regulatory reconfiguration, the major phenotypic consequences for the cell appear to depend on changes in the expression of a small number of genes with related functions.
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Affiliation(s)
- Wei Zhou
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington 98195
| | - Michael W Dorrity
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Kerry L Bubb
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195
- Department of Medicine, University of Washington, Seattle, Washington 98195
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11
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de Jongh RP, van Dijk AD, Julsing MK, Schaap PJ, de Ridder D. Designing Eukaryotic Gene Expression Regulation Using Machine Learning. Trends Biotechnol 2020; 38:191-201. [DOI: 10.1016/j.tibtech.2019.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/12/2019] [Accepted: 07/19/2019] [Indexed: 12/11/2022]
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12
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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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13
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Preferences in a trait decision determined by transcription factor variants. Proc Natl Acad Sci U S A 2018; 115:E7997-E8006. [PMID: 30068600 DOI: 10.1073/pnas.1805882115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Few mechanisms are known that explain how transcription factors can adjust phenotypic outputs to accommodate differing environments. In Saccharomyces cerevisiae, the decision to mate or invade relies on environmental cues that converge on a shared transcription factor, Ste12. Specificity toward invasion occurs via Ste12 binding cooperatively with the cofactor Tec1. Here, we determine the range of phenotypic outputs (mating vs. invasion) of thousands of DNA-binding domain variants in Ste12 to understand how preference for invasion may arise. We find that single amino acid changes in the DNA-binding domain can shift the preference of yeast toward either mating or invasion. These mutations define two distinct regions of this domain, suggesting alternative modes of DNA binding for each trait. We characterize the DNA-binding specificity of wild-type Ste12 to identify a strong preference for spacing and orientation of both homodimeric and heterodimeric sites. Ste12 mutants that promote hyperinvasion in a Tec1-independent manner fail to bind cooperative sites with Tec1 and bind to unusual dimeric Ste12 sites composed of one near-perfect and one highly degenerate site. We propose a model in which Ste12 alone may have evolved to activate invasion genes, which could explain how preference for invasion arose in the many fungal pathogens that lack Tec1.
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14
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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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15
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Liu W, Luo Z, Wang Y, Pham NT, Tuck L, Pérez-Pi I, Liu L, Shen Y, French C, Auer M, Marles-Wright J, Dai J, Cai Y. Rapid pathway prototyping and engineering using in vitro and in vivo synthetic genome SCRaMbLE-in methods. Nat Commun 2018; 9:1936. [PMID: 29789543 PMCID: PMC5964202 DOI: 10.1038/s41467-018-04254-0] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/11/2018] [Indexed: 12/11/2022] Open
Abstract
Exogenous pathway optimization and chassis engineering are two crucial methods for heterologous pathway expression. The two methods are normally carried out step-wise and in a trial-and-error manner. Here we report a recombinase-based combinatorial method (termed "SCRaMbLE-in") to tackle both challenges simultaneously. SCRaMbLE-in includes an in vitro recombinase toolkit to rapidly prototype and diversify gene expression at the pathway level and an in vivo genome reshuffling system to integrate assembled pathways into the synthetic yeast genome while combinatorially causing massive genome rearrangements in the host chassis. A set of loxP mutant pairs was identified to maximize the efficiency of the in vitro diversification. Exemplar pathways of β-carotene and violacein were successfully assembled, diversified, and integrated using this SCRaMbLE-in method. High-throughput sequencing was performed on selected engineered strains to reveal the resulting genotype-to-phenotype relationships. The SCRaMbLE-in method proves to be a rapid, efficient, and universal method to fast track the cycle of engineering biology.
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Affiliation(s)
- Wei Liu
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Zhouqing Luo
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Yun Wang
- BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, 518120, Shenzhen, China
| | - Nhan T Pham
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Laura Tuck
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Irene Pérez-Pi
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Longying Liu
- BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, 518120, Shenzhen, China
| | - Yue Shen
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK.,BGI-Shenzhen, Beishan Industrial Zone, 518083, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Jinsha Road, 518120, Shenzhen, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Jinsha Road, 518120, Shenzhen, China.,Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Chris French
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Manfred Auer
- School of Biological Sciences, The King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK.,Edinburgh Medical School, Biomedical Sciences, The King's Buildings, Edinburgh, EH9 3BF, UK
| | - Jon Marles-Wright
- School of Natural and Environmental Sciences, Devonshire Building, Newcastle University, Newcastle upon, Tyne, NE1 7RX, UK
| | - Junbiao Dai
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China.
| | - Yizhi Cai
- Center for Synthetic Genomics, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China. .,Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK.
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Dossani ZY, Reider Apel A, Szmidt-Middleton H, Hillson NJ, Deutsch S, Keasling JD, Mukhopadhyay A. A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering. Yeast 2017; 35:273-280. [PMID: 29084380 PMCID: PMC5873372 DOI: 10.1002/yea.3292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/08/2017] [Accepted: 10/19/2017] [Indexed: 12/28/2022] Open
Abstract
Despite the need for inducible promoters in strain development efforts, the majority of engineering in Saccharomyces cerevisiae continues to rely on a few constitutively active or inducible promoters. Building on advances that use the modular nature of both transcription factors and promoter regions, we have built a library of hybrid promoters that are regulated by a synthetic transcription factor. The hybrid promoters consist of native S. cerevisiae promoters, in which the operator regions have been replaced with sequences that are recognized by the bacterial LexA DNA binding protein. Correspondingly, the synthetic transcription factor (TF) consists of the DNA binding domain of the LexA protein, fused with the human estrogen binding domain and the viral activator domain, VP16. The resulting system with a bacterial DNA binding domain avoids the transcription of native S. cerevisiae genes, and the hybrid promoters can be induced using estradiol, a compound with no detectable impact on S. cerevisiae physiology. Using combinations of one, two or three operator sequence repeats and a set of native S. cerevisiae promoters, we obtained a series of hybrid promoters that can be induced to different levels, using the same synthetic TF and a given estradiol. This set of promoters, in combination with our synthetic TF, has the potential to regulate numerous genes or pathways simultaneously, to multiple desired levels, in a single strain.
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Affiliation(s)
- Zain Y Dossani
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Amanda Reider Apel
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Heather Szmidt-Middleton
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Nathan J Hillson
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,DOE Joint Genome Institute, Walnut Creek, California, USA.,DOE Agile BioFoundry, Emeryville, California, USA
| | - Samuel Deutsch
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,DOE Joint Genome Institute, Walnut Creek, California, USA.,DOE Agile BioFoundry, Emeryville, California, USA
| | - Jay D Keasling
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220 Kemitorvet, 2800Kgs, Lyngby, Denmark
| | - Aindrila Mukhopadhyay
- DOE Joint Bioenergy Institute, Emeryville, California, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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