1
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Fenelon KD, Krause J, Koromila T. Opticool: Cutting-edge transgenic optical tools. PLoS Genet 2024; 20:e1011208. [PMID: 38517915 PMCID: PMC10959397 DOI: 10.1371/journal.pgen.1011208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024] Open
Abstract
Only a few short decades have passed since the sequencing of GFP, yet the modern repertoire of transgenically encoded optical tools implies an exponential proliferation of ever improving constructions to interrogate the subcellular environment. A myriad of tags for labeling proteins, RNA, or DNA have arisen in the last few decades, facilitating unprecedented visualization of subcellular components and processes. Development of a broad array of modern genetically encoded sensors allows real-time, in vivo detection of molecule levels, pH, forces, enzyme activity, and other subcellular and extracellular phenomena in ever expanding contexts. Optogenetic, genetically encoded optically controlled manipulation systems have gained traction in the biological research community and facilitate single-cell, real-time modulation of protein function in vivo in ever broadening, novel applications. While this field continues to explosively expand, references are needed to assist scientists seeking to use and improve these transgenic devices in new and exciting ways to interrogate development and disease. In this review, we endeavor to highlight the state and trajectory of the field of in vivo transgenic optical tools.
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Affiliation(s)
- Kelli D. Fenelon
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Julia Krause
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
| | - Theodora Koromila
- Department of Biology, University of Texas at Arlington, Arlington, Texas, United States of America
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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2
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Gligorovski V, Rahi SJ. Construction and Characterization of Light-Responsive Transcriptional Systems. Methods Mol Biol 2024; 2844:261-275. [PMID: 39068346 DOI: 10.1007/978-1-0716-4063-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Optogenetic tools provide a means for controlling cellular processes that is rapid, noninvasive, and spatially and temporally precise. With the increase in available optogenetic systems, quantitative comparisons of their performances become important to guide experiments. In this chapter, we first discuss how photoreceptors can be repurposed for light-mediated control of transcription. Then, we provide a detailed protocol for characterizing light-regulated transcriptional systems in budding yeast using fluorescence time-lapse microscopy and mathematical modeling, expanding on our recent publication (Gligorovski et al., Nat Commun 14:3810, 2023).
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Affiliation(s)
- Vojislav Gligorovski
- 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.
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3
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Joest EF, Tampé R. Design principles for engineering light-controlled antibodies. Trends Biotechnol 2023; 41:1501-1517. [PMID: 37507295 DOI: 10.1016/j.tibtech.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023]
Abstract
Engineered antibodies are essential tools for research and advanced pharmacy. In the development of therapeutics, antibodies are excellent candidates as they offer both target recognition and modulation. Thanks to the latest advances in biotechnology, light-activated antibody fragments can be constructed to control spontaneous antigen interaction with high spatiotemporal precision. To implement conditional antigen binding, several optogenetic and optochemical engineering concepts have recently been developed. Here, we highlight the various strategies and discuss the features of opto-conditional antibodies. Each concept offers intrinsic advantages beneficial to different applications. In summary, the novel design approaches constitute a complementary toolset to promote current and upcoming antibody technologies with ultimate precision.
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Affiliation(s)
- Eike F Joest
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany.
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt a.M., Germany.
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4
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Bezold F, Scheffer J, Wendering P, Razaghi-Moghadam Z, Trauth J, Pook B, Nußhär H, Hasenjäger S, Nikoloski Z, Essen LO, Taxis C. Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast. Metab Eng 2023; 79:97-107. [PMID: 37422133 DOI: 10.1016/j.ymben.2023.06.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/10/2023]
Abstract
Dynamic metabolic engineering is a strategy to switch key metabolic pathways in microbial cell factories from biomass generation to accumulation of target products. Here, we demonstrate that optogenetic intervention in the cell cycle of budding yeast can be used to increase production of valuable chemicals, such as the terpenoid β-carotene or the nucleoside analog cordycepin. We achieved optogenetic cell-cycle arrest in the G2/M phase by controlling activity of the ubiquitin-proteasome system hub Cdc48. To analyze the metabolic capacities in the cell cycle arrested yeast strain, we studied their proteomes by timsTOF mass spectrometry. This revealed widespread, but highly distinct abundance changes of metabolic key enzymes. Integration of the proteomics data in protein-constrained metabolic models demonstrated modulation of fluxes directly associated with terpenoid production as well as metabolic subsystems involved in protein biosynthesis, cell wall synthesis, and cofactor biosynthesis. These results demonstrate that optogenetically triggered cell cycle intervention is an option to increase the yields of compounds synthesized in a cellular factory by reallocation of metabolic resources.
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Affiliation(s)
- Filipp Bezold
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Johannes Scheffer
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Philipp Wendering
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Zahra Razaghi-Moghadam
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Jonathan Trauth
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Bastian Pook
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Hagen Nußhär
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Sophia Hasenjäger
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany
| | - Zoran Nikoloski
- Systems Biology and Mathematical Modeling, Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany; Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032, Marburg, Germany.
| | - Christof Taxis
- Department of Biology/Genetics, Philipps-University Marburg, 35032, Marburg, Germany; School of Science and Technology, University Siegen, 57076, Siegen, Germany.
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5
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Hasenjäger S, Bologna A, Essen LO, Spadaccini R, Taxis C. C-terminal sequence stability profiling in Saccharomyces cerevisiae reveals protective protein quality control pathways. J Biol Chem 2023; 299:105166. [PMID: 37595870 PMCID: PMC10493509 DOI: 10.1016/j.jbc.2023.105166] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/22/2023] [Accepted: 08/09/2023] [Indexed: 08/20/2023] Open
Abstract
Protein quality control (PQC) mechanisms are essential for degradation of misfolded or dysfunctional proteins. An essential part of protein homeostasis is recognition of defective proteins by PQC components and their elimination by the ubiquitin-proteasome system, often concentrating on protein termini as indicators of protein integrity. Changes in amino acid composition of C-terminal ends arise through protein disintegration, alternative splicing, or during the translation step of protein synthesis from premature termination or translational stop-codon read-through. We characterized reporter protein stability using light-controlled exposure of the random C-terminal peptide collection (CtPC) in budding yeast revealing stabilizing and destabilizing features of amino acids at positions -5 to -1 of the C terminus. The (de)stabilization properties of CtPC-degrons depend on amino acid identity, position, as well as composition of the C-terminal sequence and are transferable. Evolutionary pressure toward stable proteins in yeast is evidenced by amino acid residues under-represented in cytosolic and nuclear proteins at corresponding C-terminal positions, but over-represented in unstable CtPC-degrons, and vice versa. Furthermore, analysis of translational stop-codon read-through peptides suggested that such extended proteins have destabilizing C termini. PQC pathways targeting CtPC-degrons involved the ubiquitin-protein ligase Doa10 and the cullin-RING E3 ligase SCFDas1 (Skp1-Cullin-F-box protein). Overall, our data suggest a proteome protection mechanism that targets proteins with unnatural C termini by recognizing a surprisingly large number of C-terminal sequence variants.
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Affiliation(s)
- Sophia Hasenjäger
- Department of Biology/Genetics, Philipps-University Marburg, Marburg, Germany
| | - Andrea Bologna
- Department of Science and Technology, Universita' Degli Studi Del Sannio, Benevento, Italy
| | - Lars-Oliver Essen
- Department of Chemistry/Biochemistry, Philipps-University Marburg, Marburg, Germany
| | - Roberta Spadaccini
- Department of Science and Technology, Universita' Degli Studi Del Sannio, Benevento, Italy; Department of Chemistry/Biochemistry, Philipps-University Marburg, Marburg, Germany
| | - Christof Taxis
- Department of Medicine, Health and Medical University, Erfurt, Germany.
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6
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Mao M, Qian Y, Zhang W, Zhou S, Wang Z, Chen X, Yang Y. Controlling protein stability with SULI, a highly sensitive tag for stabilization upon light induction. Nat Commun 2023; 14:2172. [PMID: 37061509 PMCID: PMC10105765 DOI: 10.1038/s41467-023-37830-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/03/2023] [Indexed: 04/17/2023] Open
Abstract
Optogenetics tools for precise temporal and spatial control of protein abundance are valuable in studying diverse complex biological processes. In the present study, we engineer a monomeric tag of stabilization upon light induction (SULI) for yeast and zebrafish based on a single light-oxygen-voltage domain from Neurospora crassa. Proteins of interest fused with SULI are stable upon light illumination but are readily degraded after transfer to dark conditions. SULI shows a high dynamic range and a high tolerance to fusion at different positions of the target protein. Further studies reveal that SULI-mediated degradation occurs through a lysine ubiquitination-independent proteasome pathway. We demonstrate the usefulness of SULI in controlling the cell cycle in yeast and regulating protein stability in zebrafish, respectively. Overall, our data indicate that SULI is a simple and robust tool to quantitatively and spatiotemporally modulate protein levels for biotechnological or biomedical applications.
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Affiliation(s)
- Miaowei Mao
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yajie Qian
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Wenyao Zhang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Siyu Zhou
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Zefeng Wang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xianjun Chen
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
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7
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de Wit E, Nora EP. New insights into genome folding by loop extrusion from inducible degron technologies. Nat Rev Genet 2023; 24:73-85. [PMID: 36180596 DOI: 10.1038/s41576-022-00530-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2022] [Indexed: 01/24/2023]
Abstract
Chromatin folds into dynamic loops that often span hundreds of kilobases and physically wire distant loci together for gene regulation. These loops are continuously created, extended and positioned by structural maintenance of chromosomes (SMC) protein complexes, such as condensin and cohesin, and their regulators, including CTCF, in a highly dynamic process known as loop extrusion. Genetic loss of extrusion factors is lethal, complicating their study. Inducible protein degradation technologies enable the depletion of loop extrusion factors within hours, leading to the rapid reconfiguration of chromatin folding. Here, we review how these technologies have changed our understanding of genome organization, upsetting long-held beliefs on its role in transcription. Finally, we examine recent models that attempt to reconcile observations after chronic versus acute perturbations, and discuss future developments in this rapidly developing field of research.
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Affiliation(s)
- Elzo de Wit
- Division of Gene Regulation, Oncode Institute, Amsterdam, the Netherlands.
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, the Netherlands.
| | - Elphège P Nora
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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8
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Optogenetic tools for microbial synthetic biology. Biotechnol Adv 2022; 59:107953. [DOI: 10.1016/j.biotechadv.2022.107953] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/09/2022] [Accepted: 04/04/2022] [Indexed: 12/22/2022]
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9
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Hoffman SM, Tang AY, Avalos JL. Optogenetics Illuminates Applications in Microbial Engineering. Annu Rev Chem Biomol Eng 2022; 13:373-403. [PMID: 35320696 DOI: 10.1146/annurev-chembioeng-092120-092340] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Optogenetics has been used in a variety of microbial engineering applications, such as chemical and protein production, studies of cell physiology, and engineered microbe-host interactions. These diverse applications benefit from the precise spatiotemporal control that light affords, as well as its tunability, reversibility, and orthogonality. This combination of unique capabilities has enabled a surge of studies in recent years investigating complex biological systems with completely new approaches. We briefly describe the optogenetic tools that have been developed for microbial engineering, emphasizing the scientific advancements that they have enabled. In particular, we focus on the unique benefits and applications of implementing optogenetic control, from bacterial therapeutics to cybergenetics. Finally, we discuss future research directions, with special attention given to the development of orthogonal multichromatic controls. With an abundance of advantages offered by optogenetics, the future is bright in microbial engineering. Expected final online publication date for the Annual Review of Chemical and Biomolecular Engineering, Volume 13 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Shannon M Hoffman
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , ,
| | - Allison Y Tang
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , ,
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA; , , .,The Andlinger Center for Energy and the Environment, Department of Molecular Biology, and High Meadows Environmental Institute, Princeton University, Princeton, New Jersey, USA
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10
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Recent advances in construction and regulation of yeast cell factories. World J Microbiol Biotechnol 2022; 38:57. [PMID: 35174424 DOI: 10.1007/s11274-022-03241-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/30/2022] [Indexed: 01/12/2023]
Abstract
The past decade has witnessed the rapid progress in development of synthetic biology, and advances in construction of yeast cell factories open vast opportunities for green and sustainable production of chemicals. Focusing on the progress in yeast engineering for production of plant natural products in the last 5 years, this review introduces different yeast chassis used for cell factory construction, including Saccharomyces cerevisiae, Yarrowia lipolytica and Komagataella phaffii, together with the emerging genome editing tools. The metabolic regulation strategies developed for yeast engineering are highlighted, such as subcellular pathway localization dynamic regulation, and transporter engineering. C1-based chemical bioproduction by engineered yeast is also covered. Finally, the existing challenges and future prospects in creating efficient yeast cell factories are summarized.
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11
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Pook B, Goenrich J, Hasenjäger S, Essen LO, Spadaccini R, Taxis C. An Optogenetic Toolbox for Synergistic Regulation of Protein Abundance. ACS Synth Biol 2021; 10:3411-3421. [PMID: 34797069 DOI: 10.1021/acssynbio.1c00350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Optogenetic tools have been proven to be useful in regulating cellular processes via an external signal. Light can be applied with high spatial and temporal precision as well as easily modulated in quantity and quality. Natural photoreceptors of the light oxygen voltage (LOV) domain family have been characterized in depth, especially the LOV2 domain of Avena sativa (As) phototropin 1 and its derivatives. Information on the behavior of LOV2 variants with changes in the photocycle or the light response has been recorded. Here, we applied well-described photocycle mutations on the AsLOV2 domain of a photosensitive transcription factor (psTF) as well as its variant that is part of the photosensitive degron (psd) psd3 in Saccharomyces cerevisiae. In vivo and in vitro measurements revealed that each photoreceptor component of the light-sensitive transcription factor and the psd3 module can be modulated in its light sensitivity by mutations that are known to prolong or shorten the dark-reversion time of AsLOV2. Yet, only two of the mutations showed differences in the in vivo behavior in the context of the psd3 module. For the AsLOV2 domain in the context of the psTF, we observed different characteristics for all four variants. Molecular dynamics simulations showed distinct influences of the shortened Jα helix and the V416L mutation in the context of the psd3 photoreceptor. In conclusion, we demonstrated the tunability of two optogenetic tools with a set of mutations that affect the photocycle of the inherent photoreceptors. As these optogenetic tools are concurrent in their action, pleiotropic effects on target protein abundance are achievable with the simultaneous action of the diverse photoreceptor variants.
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Affiliation(s)
- Bastian Pook
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032 Marburg, Germany
| | - Juri Goenrich
- Department of Biology/Genetics, Philipps-University Marburg, 35043 Marburg, Germany
| | - Sophia Hasenjäger
- Department of Biology/Genetics, Philipps-University Marburg, 35043 Marburg, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-University Marburg, 35032 Marburg, Germany
| | - Roberta Spadaccini
- Department of Science and Technology, Università degli Studi del Sannio, 82100 Benevento, Italy
| | - Christof Taxis
- Department of Biology/Genetics, Philipps-University Marburg, 35043 Marburg, Germany
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12
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Directed evolution approaches for optogenetic tool development. Biochem Soc Trans 2021; 49:2737-2748. [PMID: 34783342 DOI: 10.1042/bst20210700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/16/2021] [Accepted: 10/21/2021] [Indexed: 12/30/2022]
Abstract
Photoswitchable proteins enable specific molecular events occurring in complex biological settings to be probed in a rapid and reversible fashion. Recent progress in the development of photoswitchable proteins as components of optogenetic tools has been greatly facilitated by directed evolution approaches in vitro, in bacteria, or in yeast. We review these developments and suggest future directions for this rapidly advancing field.
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13
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Lindner F, Diepold A. Optogenetics in bacteria - applications and opportunities. FEMS Microbiol Rev 2021; 46:6427354. [PMID: 34791201 PMCID: PMC8892541 DOI: 10.1093/femsre/fuab055] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Optogenetics holds the promise of controlling biological processes with superb temporal and spatial resolution at minimal perturbation. Although many of the light-reactive proteins used in optogenetic systems are derived from prokaryotes, applications were largely limited to eukaryotes for a long time. In recent years, however, an increasing number of microbiologists use optogenetics as a powerful new tool to study and control key aspects of bacterial biology in a fast and often reversible manner. After a brief discussion of optogenetic principles, this review provides an overview of the rapidly growing number of optogenetic applications in bacteria, with a particular focus on studies venturing beyond transcriptional control. To guide future experiments, we highlight helpful tools, provide considerations for successful application of optogenetics in bacterial systems, and identify particular opportunities and challenges that arise when applying these approaches in bacteria.
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Affiliation(s)
- Florian Lindner
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany
| | - Andreas Diepold
- Max-Planck-Institute for Terrestrial Microbiology, Department of Ecophysiology, Karl-von-Frisch-Str. 10, 35043 Marburg, Germany.,SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
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14
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Lalwani MA, Zhao EM, Wegner SA, Avalos JL. The Neurospora crassa Inducible Q System Enables Simultaneous Optogenetic Amplification and Inversion in Saccharomyces cerevisiae for Bidirectional Control of Gene Expression. ACS Synth Biol 2021; 10:2060-2075. [PMID: 34346207 DOI: 10.1021/acssynbio.1c00229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bidirectional optogenetic control of yeast gene expression has great potential for biotechnological applications. Our group has developed optogenetic inverter circuits that activate transcription using darkness, as well as amplifier circuits that reach high expression levels under limited light. However, because both types of circuits harness Gal4p and Gal80p from the galactose (GAL) regulon they cannot be used simultaneously. Here, we apply the Q System, a transcriptional activator/inhibitor system from Neurospora crassa, to build circuits in Saccharomyces cerevisiae that are inducible using quinic acid, darkness, or blue light. We develop light-repressed OptoQ-INVRT circuits that initiate darkness-triggered transcription within an hour of induction, as well as light-activated OptoQ-AMP circuits that achieve up to 39-fold induction. The Q System does not exhibit crosstalk with the GAL regulon, allowing coutilization of OptoQ-AMP circuits with previously developed OptoINVRT circuits. As a demonstration of practical applications in metabolic engineering, we show how simultaneous use of these circuits can be used to dynamically control both growth and production to improve acetoin production, as well as enable light-tunable co-production of geraniol and linalool, two terpenoids implicated in the hoppy flavor of beer. OptoQ-AMP and OptoQ-INVRT circuits enable simultaneous optogenetic signal amplification and inversion, providing powerful additions to the yeast optogenetic toolkit.
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Affiliation(s)
- Makoto A. Lalwani
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Evan M. Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Scott A. Wegner
- Department of Molecular Biology. Princeton University, Princeton, New Jersey 08544, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology. Princeton University, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey 08544, United States
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15
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Reynders M, Trauner D. Optical control of targeted protein degradation. Cell Chem Biol 2021; 28:969-986. [PMID: 34115971 DOI: 10.1016/j.chembiol.2021.05.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/12/2021] [Accepted: 05/14/2021] [Indexed: 12/13/2022]
Abstract
Molecular glues and proteolysis targeting chimeras (PROTACs) have emerged as small-molecule tools that selectively induce the degradation of a chosen protein and have shown therapeutic promise. Recently, several approaches employing light as an additional stimulus to control induced protein degradation have been reported. Here, we analyze the principles guiding the design of such systems, provide a survey of the literature published to date, and discuss opportunities for further development. Light-responsive degraders enable the precise temporal and spatial control of protein levels, making them useful research tools but also potential candidates for human precision medicine.
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Affiliation(s)
- Martin Reynders
- Department of Chemistry, New York University, New York, NY 10003, USA; Department of Chemistry, Ludwig Maximilians University of Munich, 81377 Munich, Germany
| | - Dirk Trauner
- Department of Chemistry, New York University, New York, NY 10003, USA; Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA; NYU Neuroscience Institute, New York University School of Medicine, New York, NY 10016, USA.
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16
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A Novel Research Technology to Explore the Mystery of Traditional Chinese Medicine: Optogenetics. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021. [DOI: 10.1155/2021/6613368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Traditional Chinese medicine (TCM) is gaining increasing popularity worldwide for the function of health promotion and adjuvant therapy. However, the world's understanding of TCM is far from enough, which seriously limits the modernization and internationalization of TCM. Therefore, modern and efficient analytical methods are urgently needed to understand the mechanism of TCM. Optogenetics is one of the most prevalent technologies in the 21st century and has been used to explore life science, especially neuroscience. It already has had great influences in the study of neural circuits and animal models of mental diseases and was named “Method of the Year” by the Nature Methods journal in 2010. Increased interests occurred in the applications of optogenetics to explore a myriad of medical and mental health disorders. However, it has not so far been noticed by TCM researchers. We elaborated on an idea that introducing this technique into the field of TCM research to improve diagnosis, treatments, and evaluating the therapeutic effects. In this review, we made a systematic prospect in the theory, feasibility, and application of TCM optogenetics. We mainly focused on applying optogenetic methodologies to make a more comprehensive understanding of TCM.
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17
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Photoreaction Mechanisms of Flavoprotein Photoreceptors and Their Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:189-206. [PMID: 33398814 DOI: 10.1007/978-981-15-8763-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Three classes of flavoprotein photoreceptors, cryptochromes (CRYs), light-oxygen-voltage (LOV)-domain proteins, and blue light using FAD (BLUF)-domain proteins, have been identified that control various physiological processes in multiple organisms. Accordingly, signaling activities of photoreceptors have been intensively studied and the related mechanisms have been exploited in numerous optogenetic tools. Herein, we summarize the current understanding of photoactivation mechanisms of the flavoprotein photoreceptors and review their applications.
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18
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Nakanishi H, Yoshii T, Kawasaki S, Hayashi K, Tsutsui K, Oki C, Tsukiji S, Saito H. Light-controllable RNA-protein devices for translational regulation of synthetic mRNAs in mammalian cells. Cell Chem Biol 2021; 28:662-674.e5. [PMID: 33508227 DOI: 10.1016/j.chembiol.2021.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 10/26/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022]
Abstract
The photo-regulation of transgene expression is one effective approach in mammalian synthetic biology due to its high spatial and temporal resolution. While DNAs are mainly used as vectors, modified RNAs (modRNAs) are also useful for medical applications of synthetic biology, because they can avoid insertional mutagenesis and immunogenicity. However, the optogenetic control of modRNA-delivered transgenes is much more difficult than that of DNA-delivered transgenes. Here, we develop two types of photo-controllable translational activation systems that are compatible with modRNAs. One is composed of a heterodimerization domain-fused split translational activator protein and a photocaged heterodimerizer. The other is composed of a destabilizing domain-fused translational activator protein and a photocaged stabilizer. The destabilized type can be used for not only translational activation but also translational repression of the modRNAs. These photo-controllable translation systems will expand the application of mammalian synthetic biology research.
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Affiliation(s)
- Hideyuki Nakanishi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; Department of Biofunction Research, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University (TMDU), 2-3-10 Kanda-Surugadai, Chiyoda-ku, Tokyo 101-0062, Japan
| | - Tatsuyuki Yoshii
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Shunsuke Kawasaki
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Karin Hayashi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan
| | - Keita Tsutsui
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Choji Oki
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Shinya Tsukiji
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan; Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555, Japan
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan.
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19
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Abstract
Proteolysis Targeting Chimeras (PROTACs) are a promising technology to degrade specific target proteins. As bifunctional small molecules, PROTACs induce the ternary complex formation between an E3 ligase and a protein of interest (POI), leading to polyubiquitylation and subsequent proteasomal degradation of the protein in a catalytic fashion. We have developed a strategy to control PROTACs with the spatiotemporal precision of light, which led to light-activated versions, termed PHOTACs (PHOtochemically TArgeted Chimeras). By incorporating an azobenzene photoswitch into the PROTAC, we can reversibly control degradation of the POI, as demonstrated for BRD2-4 and FKBP12. Here, we describe our modular approach and the application of PHOTACs for the optical control of protein levels in detail. PHOTACs hold promise as both research tools and precision pharmaceutics.
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Affiliation(s)
- Martin Reynders
- Department of Chemistry, New York University, New York, NY, USA.,Department of Chemistry, Ludwig Maximilians University of Munich, Munich, Germany
| | - Dirk Trauner
- Department of Chemistry, New York University, New York, NY, USA. .,Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA. .,NYU Neuroscience Institute, New York University School of Medicine, New York, NY, USA.
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20
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Shaaya M, Fauser J, Karginov AV. Optogenetics: The Art of Illuminating Complex Signaling Pathways. Physiology (Bethesda) 2021; 36:52-60. [PMID: 33325819 DOI: 10.1152/physiol.00022.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dissection of cell signaling requires tools that can mimic spatiotemporal dynamics of individual pathways in living cells. Optogenetic methods enable manipulation of signaling processes with precise timing and local control. In this review, we describe recent optogenetic approaches for regulation of cell signaling, highlight their advantages and limitations, and discuss examples of their application.
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Affiliation(s)
- Mark Shaaya
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois
| | - Andrei V Karginov
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, College of Medicine, Chicago, Illinois.,University of Illinois Cancer Center, The University of Illinois at Chicago, Chicago, Illinois
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21
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Zhao EM, Lalwani MA, Lovelett RJ, García-Echauri SA, Hoffman SM, Gonzalez CL, Toettcher JE, Kevrekidis IG, Avalos JL. Design and Characterization of Rapid Optogenetic Circuits for Dynamic Control in Yeast Metabolic Engineering. ACS Synth Biol 2020; 9:3254-3266. [PMID: 33232598 PMCID: PMC10399620 DOI: 10.1021/acssynbio.0c00305] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The use of optogenetics in metabolic engineering for light-controlled microbial chemical production raises the prospect of utilizing control and optimization techniques routinely deployed in traditional chemical manufacturing. However, such mechanisms require well-characterized, customizable tools that respond fast enough to be used as real-time inputs during fermentations. Here, we present OptoINVRT7, a new rapid optogenetic inverter circuit to control gene expression in Saccharomyces cerevisiae. The circuit induces gene expression in only 0.6 h after switching cells from light to darkness, which is at least 6 times faster than previous OptoINVRT optogenetic circuits used for chemical production. In addition, we introduce an engineered inducible GAL1 promoter (PGAL1-S), which is stronger than any constitutive or inducible promoter commonly used in yeast. Combining OptoINVRT7 with PGAL1-S achieves strong and light-tunable levels of gene expression with as much as 132.9 ± 22.6-fold induction in darkness. The high performance of this new optogenetic circuit in controlling metabolic enzymes boosts production of lactic acid and isobutanol by more than 50% and 15%, respectively. The strength and controllability of OptoINVRT7 and PGAL1-S open the door to applying process control tools to engineered metabolisms to improve robustness and yields in microbial fermentations for chemical production.
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Affiliation(s)
- Evan M. Zhao
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Makoto A. Lalwani
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Robert J. Lovelett
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, 221 Maryland
Hall, Johns Hopkins University, 2400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Sergio A. García-Echauri
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Shannon M. Hoffman
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Christopher L. Gonzalez
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
| | - Jared E. Toettcher
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
| | - Ioannis G. Kevrekidis
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Chemical and Biomolecular Engineering, 221 Maryland
Hall, Johns Hopkins University, 2400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory
101, Princeton University, William Street, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Princeton University, Washington Road, Princeton, New Jersey 08544, United States
- The Andlinger Center for Energy and the Environment, Princeton University, 86 Olden Street, Princeton, New Jersey 08544, United States
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22
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Figueroa D, Rojas V, Romero A, Larrondo LF, Salinas F. The rise and shine of yeast optogenetics. Yeast 2020; 38:131-146. [PMID: 33119964 DOI: 10.1002/yea.3529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 12/11/2022] Open
Abstract
Optogenetics refers to the control of biological processes with light. The activation of cellular phenomena by defined wavelengths has several advantages compared with traditional chemically inducible systems, such as spatiotemporal resolution, dose-response regulation, low cost, and moderate toxic effects. Optogenetics has been successfully implemented in yeast, a remarkable biological platform that is not only a model organism for cellular and molecular biology studies, but also a microorganism with diverse biotechnological applications. In this review, we summarize the main optogenetic systems implemented in the budding yeast Saccharomyces cerevisiae, which allow orthogonal control (by light) of gene expression, protein subcellular localization, reconstitution of protein activity, and protein sequestration by oligomerization. Furthermore, we review the application of optogenetic systems in the control of metabolic pathways, heterologous protein production and flocculation. We then revise an example of a previously described yeast optogenetic switch, named FUN-LOV, which allows precise and strong activation of the target gene. Finally, we describe optogenetic systems that have not yet been implemented in yeast, which could therefore be used to expand the panel of available tools in this biological chassis. In conclusion, a wide repertoire of optogenetic systems can be used to address fundamental biological questions and broaden the biotechnological toolkit in yeast.
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Affiliation(s)
- David Figueroa
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
| | - Vicente Rojas
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andres Romero
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Luis F Larrondo
- ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile.,Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Francisco Salinas
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.,ANID - Millennium Science Initiative - Millennium Institute for Integrative Biology (iBIO), Santiago, Chile
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23
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Kichuk TC, Carrasco-López C, Avalos JL. Lights up on organelles: Optogenetic tools to control subcellular structure and organization. WIREs Mech Dis 2020; 13:e1500. [PMID: 32715616 DOI: 10.1002/wsbm.1500] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/26/2020] [Accepted: 05/31/2020] [Indexed: 12/21/2022]
Abstract
Since the neurobiological inception of optogenetics, light-controlled molecular perturbations have been applied in many scientific disciplines to both manipulate and observe cellular function. Proteins exhibiting light-sensitive conformational changes provide researchers with avenues for spatiotemporal control over the cellular environment and serve as valuable alternatives to chemically inducible systems. Optogenetic approaches have been developed to target proteins to specific subcellular compartments, allowing for the manipulation of nuclear translocation and plasma membrane morphology. Additionally, these tools have been harnessed for molecular interrogation of organelle function, location, and dynamics. Optogenetic approaches offer novel ways to answer fundamental biological questions and to improve the efficiency of bioengineered cell factories by controlling the assembly of synthetic organelles. This review first provides a summary of available optogenetic systems with an emphasis on their organelle-specific utility. It then explores the strategies employed for organelle targeting and concludes by discussing our perspective on the future of optogenetics to control subcellular structure and organization. This article is categorized under: Metabolic Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Therese C Kichuk
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - César Carrasco-López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA.,Andlinger Center for Energy and the Environment, Princeton University, Princeton, New Jersey, USA
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24
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Woloschuk RM, Reed PMM, McDonald S, Uppalapati M, Woolley GA. Yeast Two-Hybrid Screening of Photoswitchable Protein-Protein Interaction Libraries. J Mol Biol 2020; 432:3113-3126. [PMID: 32198111 DOI: 10.1016/j.jmb.2020.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 02/08/2023]
Abstract
Although widely used in the detection and characterization of protein-protein interactions, Y2H screening has been under-used for the engineering of new optogenetic tools or the improvement of existing tools. Here we explore the feasibility of using Y2H selection and screening to evaluate libraries of photoswitchable protein-protein interactions. We targeted the interaction between circularly permuted photoactive yellow protein (cPYP) and its binding partner binder of PYP dark-state (BoPD) by mutating a set of four surface residues of cPYP that contribute to the binding interface. A library of ~10,000 variants was expressed in yeast together with BoPD in a Y2H format. An initial selection for the cPYP/BoPD interaction was performed using a range of concentrations of the cPYP chromophore. As expected, the majority (>90% of cPYP variants) no longer bound to BoPD. Replica plating was then used to evaluate the photoswitchability of the surviving clones. Photoswitchable cPYP variants with BoPD affinities equal to, or higher than, native cPYP were recovered in addition to variants with altered photocycles and binders that interacted with BoPD as apo-proteins. Y2H results reflected protein-protein interaction affinity, expression, photoswitchability, and chromophore uptake, and correlated well with results obtained both in vitro and in mammalian cells. Thus, by systematic variation of selection parameters, Y2H screens can be effectively used to generate new optogenetic tools for controlling protein-protein interactions for use in diverse settings.
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Affiliation(s)
- Ryan M Woloschuk
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Canada, M5S 3H6
| | - P Maximilian M Reed
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Canada, M5S 3H6
| | - Sherin McDonald
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, Canada, S7N 5E5
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK, Canada, S7N 5E5
| | - G Andrew Woolley
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Canada, M5S 3H6.
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25
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Hepp S, Trauth J, Hasenjäger S, Bezold F, Essen LO, Taxis C. An Optogenetic Tool for Induced Protein Stabilization Based on the Phaeodactylum tricornutum Aureochrome 1a Light-Oxygen-Voltage Domain. J Mol Biol 2020; 432:1880-1900. [PMID: 32105734 DOI: 10.1016/j.jmb.2020.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/10/2020] [Accepted: 02/14/2020] [Indexed: 01/02/2023]
Abstract
Control of cellular events by optogenetic tools is a powerful approach to manipulate cellular functions in a minimally invasive manner. A common problem posed by the application of optogenetic tools is to tune the activity range to be physiologically relevant. Here, we characterized a photoreceptor of the light-oxygen-voltage (LOV) domain family of Phaeodactylum tricornutum aureochrome 1a (AuLOV) as a tool for increasing protein stability under blue light conditions in budding yeast. Structural studies of AuLOVwt, the variants AuLOVM254, and AuLOVW349 revealed alternative dimer association modes for the dark state, which differ from previously reported AuLOV dark-state structures. Rational design of AuLOV-dimer interface mutations resulted in an optimized optogenetic tool that we fused to the photoactivatable adenylyl cyclase from Beggiatoa sp. This synergistic light-regulation approach using two photoreceptors resulted in an optimized, photoactivatable adenylyl cyclase with a cyclic adenosine monophosphate production activity that matches the physiological range of Saccharomyces cerevisiae. Overall, we enlarged the optogenetic toolbox for yeast and demonstrated the importance of fine-tuning the optogenetic tool activity for successful application in cells.
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Affiliation(s)
- Sebastian Hepp
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany
| | - Jonathan Trauth
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany; Molecular Genetics, Department of Biology, Philipps Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany
| | - Sophia Hasenjäger
- Molecular Genetics, Department of Biology, Philipps Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany
| | - Filipp Bezold
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35032 Marburg, Germany; Center of Synthetic Microbiology, Philipps Universität Marburg, Hans-Meerwein- Strasse 4, 35032 Marburg, Germany.
| | - Christof Taxis
- Molecular Genetics, Department of Biology, Philipps Universität Marburg, Karl-von-Frisch-Strasse 8, 35043 Marburg, Germany.
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26
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Rogers KW, Müller P. Optogenetic approaches to investigate spatiotemporal signaling during development. Curr Top Dev Biol 2019; 137:37-77. [PMID: 32143750 DOI: 10.1016/bs.ctdb.2019.11.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Embryogenesis is coordinated by signaling pathways that pattern the developing organism. Many aspects of this process are not fully understood, including how signaling molecules spread through embryonic tissues, how signaling amplitude and dynamics are decoded, and how multiple signaling pathways cooperate to pattern the body plan. Optogenetic approaches can be used to address these questions by providing precise experimental control over a variety of biological processes. Here, we review how these strategies have provided new insights into developmental signaling and discuss how they could contribute to future investigations.
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Affiliation(s)
- Katherine W Rogers
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Patrick Müller
- Systems Biology of Development Group, Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany; Modeling Tumorigenesis Group, Translational Oncology Division, Eberhard Karls University Tübingen, Tübingen, Germany.
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27
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Guinn MT, Balázsi G. Noise-reducing optogenetic negative-feedback gene circuits in human cells. Nucleic Acids Res 2019; 47:7703-7714. [PMID: 31269201 PMCID: PMC6698750 DOI: 10.1093/nar/gkz556] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/10/2019] [Accepted: 06/12/2019] [Indexed: 12/16/2022] Open
Abstract
Gene autorepression is widely present in nature and is also employed in synthetic biology, partly to reduce gene expression noise in cells. Optogenetic systems have recently been developed for controlling gene expression levels in mammalian cells, but most have utilized activator-based proteins, neglecting negative feedback except for in silico control. Here, we engineer optogenetic gene circuits into mammalian cells to achieve noise-reduction for precise gene expression control by genetic, in vitro negative feedback. We build a toolset of these noise-reducing Light-Inducible Tuner (LITer) gene circuits using the TetR repressor fused with a Tet-inhibiting peptide (TIP) or a degradation tag through the light-sensitive LOV2 protein domain. These LITers provide a range of nearly 4-fold gene expression control and up to 5-fold noise reduction from existing optogenetic systems. Moreover, we use the LITer gene circuit architecture to control gene expression of the cancer oncogene KRAS(G12V) and study its downstream effects through phospho-ERK levels and cellular proliferation. Overall, these novel LITer optogenetic platforms should enable precise spatiotemporal perturbations for studying multicellular phenotypes in developmental biology, oncology and other biomedical fields of research.
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Affiliation(s)
- Michael Tyler Guinn
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794, USA
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Medical Scientist Training Program, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
| | - Gábor Balázsi
- Biomedical Engineering Department, Stony Brook University, Stony Brook, NY 11794, USA
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
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28
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Scheffer J, Hasenjäger S, Taxis C. Degradation of integral membrane proteins modified with the photosensitive degron module requires the cytosolic endoplasmic reticulum-associated degradation pathway. Mol Biol Cell 2019; 30:2558-2570. [PMID: 31411939 PMCID: PMC6740197 DOI: 10.1091/mbc.e18-12-0754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Protein quality mechanisms are fundamental for proteostasis of eukaryotic cells. Endoplasmic reticulum–associated degradation (ERAD) is a well-studied pathway that ensures quality control of secretory and endoplasmic reticulum (ER)–resident proteins. Different branches of ERAD are involved in degradation of malfolded secretory proteins, depending on the localization of the misfolded part, the ER lumen (ERAD-L), the ER membrane (ERAD-M), and the cytosol (ERAD-C). Here we report that modification of several ER transmembrane proteins with the photosensitive degron (psd) module resulted in light-dependent degradation of the membrane proteins via the ERAD-C pathway. We found dependency on the ubiquitylation machinery including the ubiquitin-activating enzyme Uba1, the ubiquitin-conjugating enzymes Ubc6 and Ubc7, and the ubiquitin–protein ligase Doa10. Moreover, we found involvement of the Cdc48 AAA-ATPase complex members Ufd1 and Npl4, as well as the proteasome, in degradation of Sec62-myc-psd. Thus, our work shows that ERAD-C substrates can be systematically generated via synthetic degron constructs, which facilitates future investigations of the ERAD-C pathway.
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Affiliation(s)
- Johannes Scheffer
- Department of Chemistry/Biochemistry, Philipps-University Marburg, 35043 Marburg, Germany
| | - Sophia Hasenjäger
- Department of Biology/Genetics, Philipps-University Marburg, 35043 Marburg, Germany
| | - Christof Taxis
- Department of Biology/Genetics, Philipps-University Marburg, 35043 Marburg, Germany
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29
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Hasenjäger S, Trauth J, Hepp S, Goenrich J, Essen LO, Taxis C. Optogenetic Downregulation of Protein Levels with an Ultrasensitive Switch. ACS Synth Biol 2019; 8:1026-1036. [PMID: 30955324 DOI: 10.1021/acssynbio.8b00471] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Optogenetic control of protein activity is a versatile technique to gain control over cellular processes, for example, for biomedical and biotechnological applications. Among other techniques, the regulation of protein abundance by controlling either transcription or protein stability found common use as this controls the activity of any type of target protein. Here, we report modules of an improved variant of the photosensitive degron module and a light-sensitive transcription factor, which we compared to doxycycline-dependent transcriptional control. Given their modularity the combined control of synthesis and stability of a given target protein resulted in the synergistic down regulation of its abundance by light. This combined module exhibits very high switching ratios, profound downregulation of protein abundance at low light-fluxes, and fast protein depletion kinetics. Overall, this synergistic optogenetic multistep control (SOMCo) module is easy to implement and results in a regulation of protein abundance superior to each individual component.
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Affiliation(s)
- Sophia Hasenjäger
- Department of Biology/Genetics Philipps-University Marburg Karl-vom-Frisch-Straße 8, Marburg, 35032, Germany
| | - Jonathan Trauth
- Department of Biology/Genetics Philipps-University Marburg Karl-vom-Frisch-Straße 8, Marburg, 35032, Germany
- Department of Chemistry/Biochemistry Philipps-University Marburg Hans-Meerwein-Straße 4, Marburg, 35032, Germany
| | - Sebastian Hepp
- Department of Chemistry/Biochemistry Philipps-University Marburg Hans-Meerwein-Straße 4, Marburg, 35032, Germany
| | - Juri Goenrich
- Department of Biology/Genetics Philipps-University Marburg Karl-vom-Frisch-Straße 8, Marburg, 35032, Germany
| | - Lars-Oliver Essen
- Department of Chemistry/Biochemistry Philipps-University Marburg Hans-Meerwein-Straße 4, Marburg, 35032, Germany
| | - Christof Taxis
- Department of Biology/Genetics Philipps-University Marburg Karl-vom-Frisch-Straße 8, Marburg, 35032, Germany
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30
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Abstract
With the rapid development of DNA synthesis and next-generation sequencing, synthetic biology that aims to standardize, modularize, and innovate cellular functions, has achieved vast progress. Here we review key advances in synthetic biology of the yeast Saccharomyces cerevisiae, which serves as an important eukaryal model organism and widely applied cell factory. This covers the development of new building blocks, i.e., promoters, terminators and enzymes, pathway engineering, tools developments, and gene circuits utilization. We will also summarize impacts of synthetic biology on both basic and applied biology, and end with further directions for advancing synthetic biology in yeast.
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Affiliation(s)
- Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing Key Laboratory of Bioprocess , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Yueping Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing Key Laboratory of Bioprocess , Beijing University of Chemical Technology , Beijing 100029 , China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing Key Laboratory of Bioprocess , Beijing University of Chemical Technology , Beijing 100029 , China.,Department of Biology and Biological Engineering , Chalmers University of Technology , Gothenburg SE41296 , Sweden.,Novo Nordisk Foundation Center for Biosustainability , Technical University of Denmark , Kongens Lyngby DK2800 , Denmark
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31
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Liu Z, Zhang J, Jin J, Geng Z, Qi Q, Liang Q. Programming Bacteria With Light-Sensors and Applications in Synthetic Biology. Front Microbiol 2018; 9:2692. [PMID: 30467500 PMCID: PMC6236058 DOI: 10.3389/fmicb.2018.02692] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/22/2018] [Indexed: 12/11/2022] Open
Abstract
Photo-receptors are widely present in both prokaryotic and eukaryotic cells, which serves as the foundation of tuning cell behaviors with light. While practices in eukaryotic cells have been relatively established, trials in bacterial cells have only been emerging in the past few years. A number of light sensors have been engineered in bacteria cells and most of them fall into the categories of two-component and one-component systems. Such a sensor toolbox has enabled practices in controlling synthetic circuits at the level of transcription and protein activity which is a major topic in synthetic biology, according to the central dogma. Additionally, engineered light sensors and practices of tuning synthetic circuits have served as a foundation for achieving light based real-time feedback control. Here, we review programming bacteria cells with light, introducing engineered light sensors in bacteria and their applications, including tuning synthetic circuits and achieving feedback controls over microbial cell culture.
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Affiliation(s)
- Zedao Liu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Jizhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Jiao Jin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Zilong Geng
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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32
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Fungal Light-Oxygen-Voltage Domains for Optogenetic Control of Gene Expression and Flocculation in Yeast. mBio 2018; 9:mBio.00626-18. [PMID: 30065085 PMCID: PMC6069114 DOI: 10.1128/mbio.00626-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Optogenetic switches permit accurate control of gene expression upon light stimulation. These synthetic switches have become a powerful tool for gene regulation, allowing modulation of customized phenotypes, overcoming the obstacles of chemical inducers, and replacing their use by an inexpensive resource: light. In this work, we implemented FUN-LOV, an optogenetic switch based on the photon-regulated interaction of WC-1 and VVD, two LOV (light-oxygen-voltage) blue-light photoreceptors from the fungus Neurospora crassa. When tested in yeast, FUN-LOV yields light-controlled gene expression with exquisite temporal resolution and a broad dynamic range of over 1,300-fold, as measured by a luciferase reporter. We also tested the FUN-LOV switch for heterologous protein expression in Saccharomyces cerevisiae, where Western blot analysis confirmed strong induction upon light stimulation, surpassing by 2.5 times the levels achieved with a classic GAL4/galactose chemical-inducible system. Additionally, we utilized FUN-LOV to control the ability of yeast cells to flocculate. Light-controlled expression of the flocculin-encoding gene FLO1, by the FUN-LOV switch, yielded flocculation in light (FIL), whereas the light-controlled expression of the corepressor TUP1 provided flocculation in darkness (FID). Altogether, the results reveal the potential of the FUN-LOV optogenetic switch to control two biotechnologically relevant phenotypes such as heterologous protein expression and flocculation, paving the road for the engineering of new yeast strains for industrial applications. Importantly, FUN-LOV’s ability to accurately manipulate gene expression, with a high temporal dynamic range, can be exploited in the analysis of diverse biological processes in various organisms. Optogenetic switches are molecular devices which allow the control of different cellular processes by light, such as gene expression, providing a versatile alternative to chemical inducers. Here, we report a novel optogenetic switch (FUN-LOV) based on the LOV domain interaction of two blue-light photoreceptors (WC-1 and VVD) from the fungus N. crassa. In yeast cells, FUN-LOV allowed tight regulation of gene expression, with low background in darkness and a highly dynamic and potent control by light. We used FUN-LOV to optogenetically manipulate, in yeast, two biotechnologically relevant phenotypes, heterologous protein expression and flocculation, resulting in strains with potential industrial applications. Importantly, FUN-LOV can be implemented in diverse biological platforms to orthogonally control a multitude of cellular processes.
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33
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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34
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Natsume T, Kanemaki MT. Conditional Degrons for Controlling Protein Expression at the Protein Level. Annu Rev Genet 2018; 51:83-102. [PMID: 29178817 DOI: 10.1146/annurev-genet-120116-024656] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The conditional depletion of a protein of interest (POI) is useful not only for loss-of-function studies, but also for the modulation of biological pathways. Technologies that work at the level of DNA, mRNA, and protein are available for temporal protein depletion. Compared with technologies targeting the pretranslation steps, direct protein depletion (or protein knockdown approaches) is advantageous in terms of specificity, reversibility, and time required for depletion, which can be achieved by fusing a POI with a protein domain called a degron that induces rapid proteolysis of the fusion protein. Conditional degrons can be activated or inhibited by temperature, small molecules, light, or the expression of another protein. The conditional degron-based technologies currently available are described and discussed.
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Affiliation(s)
- Toyoaki Natsume
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
| | - Masato T Kanemaki
- Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka 411-8540, Japan;
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35
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Zhao EM, Zhang Y, Mehl J, Park H, Lalwani MA, Toettcher JE, Avalos JL. Optogenetic regulation of engineered cellular metabolism for microbial chemical production. Nature 2018; 555:683-687. [PMID: 29562237 PMCID: PMC5876151 DOI: 10.1038/nature26141] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 02/13/2018] [Indexed: 12/29/2022]
Abstract
The optimization of engineered metabolic pathways requires careful control over the levels and timing of metabolic enzyme expression1-4. Optogenetic tools are ideal for achieving such precise control, as light can be applied and removed instantly without complex media changes. Here we show that light-controlled transcription can be used to enhance the biosynthesis of valuable products in engineered Saccharomyces cerevisiae. We introduce new optogenetic circuits to shift cells from a light-induced growth phase to a darkness-induced production phase, which allows us to control fermentation purely with light. Furthermore, optogenetic control of engineered pathways enables a new mode of bioreactor operation using periodic light pulses to tune enzyme expression during the production phase of fermentation to increase yields. Using these advances, we control the mitochondrial isobutanol pathway to produce up to 8.49 ± 0.31 g/L of isobutanol and 2.38 ± 0.06 g/L of 2-methyl-1-butanol micro-aerobically from glucose. These results make a compelling case for the application of optogenetics to metabolic engineering for valuable products.
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Affiliation(s)
- Evan M Zhao
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Yanfei Zhang
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Justin Mehl
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Helen Park
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Makoto A Lalwani
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, 140 Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey 08544, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 25 William Street, Princeton, New Jersey 08544, USA.,The Andlinger Center for Energy and the Environment, Princeton University, 86 Olden Street, Princeton, New Jersey 08544, USA
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36
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Abstract
The ubiquitin-proteasome system (UPS) controls cellular functions by maintenance of a functional proteome and degradation of key regulatory proteins. Central to the UPS is the proteasome that adjusts the abundance of numerous proteins, thereby safeguarding their activity or initiating regulatory events. Here, we demonstrate that the essential Saccharomyces cerevisiae protein Yjr141w/Ipa1 (Important for cleavage and PolyAdenylation) belongs to the HECT_2 (homologous to E6-AP carboxyl terminus_2) family. We found that five cysteine residues within the HECT_2 family signature and the C-terminus are essential for Ipa1 activity. Furthermore, Ipa1 interacts with several ubiquitin-conjugating enzymes in vivo and localizes to the cytosol and nucleus. Importantly, Ipa1 has an impact on proteasome activity, which is indicated by the activation of the Rpn4 regulon as well as by decreased turnover of destabilized proteasome substrates in an IPA1 mutant. These changes in proteasome activity might be connected to reduced maturation or modification of proteasomal core particle proteins. Our results highlight the influence of Ipa1 on the UPS. The conservation within the HECT_2 family and the connection of the human HECT_2 family member to an age-related degeneration disease might suggest that HECT_2 family members share a conserved function linked to proteasome activity.
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37
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van Haren J, Charafeddine RA, Ettinger A, Wang H, Hahn KM, Wittmann T. Local control of intracellular microtubule dynamics by EB1 photodissociation. Nat Cell Biol 2018; 20:252-261. [PMID: 29379139 PMCID: PMC5826794 DOI: 10.1038/s41556-017-0028-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 12/13/2017] [Indexed: 12/18/2022]
Abstract
End-binding proteins, EBs, are adaptors that recruit functionally diverse +TIP proteins to growing microtubule plus ends. To test with high spatial and temporal accuracy how, when and where +TIP protein complexes contribute to dynamic cell biology, we developed a photo-inactivated EB1 variant (π-EB1) by inserting a blue light-sensitive protein-protein interaction module between the microtubule- and +TIP-binding domains of EB1. π-EB1 replaces endogenous EB1 function in the absence of blue light. In contrast, blue light-mediated π-EB1 photo-dissociation results in rapid +TIP complex disassembly, and acutely and reversibly attenuates microtubule growth independent of microtubule end association of the microtubule polymerase CKAP5 (ch-TOG, XMAP215). Local π-EB1 photo-dissociation allows subcellular microtubule dynamics control at the second and micrometre scale, and elicits aversive turning of migrating cancer cells. Importantly, light-mediated domain splitting can serve as template to optically control other intracellular protein activities.
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Affiliation(s)
- Jeffrey van Haren
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Rabab A Charafeddine
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Andreas Ettinger
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA.,Institute of Epigenetics and Stem Cells, Helmholtz Center Munich, München, Germany
| | - Hui Wang
- University of North Carolina, Chapel Hill, NC, USA
| | - Klaus M Hahn
- University of North Carolina, Chapel Hill, NC, USA
| | - Torsten Wittmann
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA.
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38
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Besada-Lombana PB, McTaggart TL, Da Silva NA. Molecular tools for pathway engineering in Saccharomyces cerevisiae. Curr Opin Biotechnol 2017; 53:39-49. [PMID: 29274630 DOI: 10.1016/j.copbio.2017.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 12/26/2022]
Abstract
Molecular tools for the regulation of protein expression in Saccharomyces cerevisiae have contributed to rapid advances in pathway engineering for this yeast. This review considers new and enhanced additions to this toolbox, focusing on experimental approaches to modulate enzyme synthesis and enzyme fate. Methods for genome engineering, regulation of transcription, post-translational protein localization, and combinatorial screening and sensing in S. cerevisiae are highlighted, and promising new approaches are introduced.
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Affiliation(s)
- Pamela B Besada-Lombana
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA
| | - Tami L McTaggart
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA
| | - Nancy A Da Silva
- Department of Chemical Engineering and Materials Science, University of California, Irvine, CA 92697-2575, USA.
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39
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Strategies for the photo-control of endogenous protein activity. Curr Opin Struct Biol 2017; 45:53-58. [DOI: 10.1016/j.sbi.2016.11.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/13/2016] [Indexed: 11/21/2022]
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40
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Papagiannakis A, de Jonge JJ, Zhang Z, Heinemann M. Quantitative characterization of the auxin-inducible degron: a guide for dynamic protein depletion in single yeast cells. Sci Rep 2017; 7:4704. [PMID: 28680098 PMCID: PMC5498663 DOI: 10.1038/s41598-017-04791-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/22/2017] [Indexed: 11/24/2022] Open
Abstract
Perturbations are essential for the interrogation of biological systems. The auxin-inducible degron harbors great potential for dynamic protein depletion in yeast. Here, we thoroughly and quantitatively characterize the auxin-inducible degron in single yeast cells. We show that an auxin concentration of 0.25 mM is necessary for fast and uniform protein depletion between single cells, and that in mother cells proteins are depleted faster than their daughters. Although, protein recovery starts immediately after removal of auxin, it takes multiple generations before equilibrium is reached between protein synthesis and dilution, which is when the original protein levels are restored. Further, we found that blue light, used for GFP excitation, together with auxin results in growth defects, caused by the photo-destruction of auxin to its toxic derivatives, which can be avoided if indole-free auxin substitutes are used. Our work provides guidelines for the successful combination of microscopy, microfluidics and the auxin-inducible degron, offering the yeast community an unprecedented tool for dynamic perturbations on the single cell level.
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Affiliation(s)
- Alexandros Papagiannakis
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Janeska J de Jonge
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Zheng Zhang
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Matthias Heinemann
- Molecular Systems Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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41
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The Mitotic Exit Network Regulates Spindle Pole Body Selection During Sporulation of Saccharomyces cerevisiae. Genetics 2017; 206:919-937. [PMID: 28450458 DOI: 10.1534/genetics.116.194522] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 04/11/2017] [Indexed: 01/11/2023] Open
Abstract
Age-based inheritance of centrosomes in eukaryotic cells is associated with faithful chromosome distribution in asymmetric cell divisions. During Saccharomyces cerevisiae ascospore formation, such an inheritance mechanism targets the yeast centrosome equivalents, the spindle pole bodies (SPBs) at meiosis II onset. Decreased nutrient availability causes initiation of spore formation at only the younger SPBs and their associated genomes. This mechanism ensures encapsulation of nonsister genomes, which preserves genetic diversity and provides a fitness advantage at the population level. Here, by usage of an enhanced system for sporulation-induced protein depletion, we demonstrate that the core mitotic exit network (MEN) is involved in age-based SPB selection. Moreover, efficient genome inheritance requires Dbf2/20-Mob1 during a late step in spore maturation. We provide evidence that the meiotic functions of the MEN are more complex than previously thought. In contrast to mitosis, completion of the meiotic divisions does not strictly rely on the MEN whereas its activity is required at different time points during spore development. This is reminiscent of vegetative MEN functions in spindle polarity establishment, mitotic exit, and cytokinesis. In summary, our investigation contributes to the understanding of age-based SPB inheritance during sporulation of S. cerevisiae and provides general insights on network plasticity in the context of a specialized developmental program. Moreover, the improved system for a developmental-specific tool to induce protein depletion will be useful in other biological contexts.
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42
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Endo M, Ozawa T. Strategies for development of optogenetic systems and their applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2017. [DOI: 10.1016/j.jphotochemrev.2016.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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43
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Salinas F, Rojas V, Delgado V, Agosin E, Larrondo LF. Optogenetic switches for light-controlled gene expression in yeast. Appl Microbiol Biotechnol 2017; 101:2629-2640. [DOI: 10.1007/s00253-017-8178-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/01/2017] [Accepted: 02/03/2017] [Indexed: 02/06/2023]
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44
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Taxis C. Development of a Synthetic Switch to Control Protein Stability in Eukaryotic Cells with Light. Methods Mol Biol 2017; 1596:241-255. [PMID: 28293891 DOI: 10.1007/978-1-4939-6940-1_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
In eukaryotic cells, virtually all regulatory processes are influenced by proteolysis. Thus, synthetic control of protein stability is a powerful approach to influence cellular behavior. To achieve this, selected target proteins are modified with a conditional degradation sequence (degron) that responds to a distinct signal. For development of a synthetic degron, an appropriate sensor domain is fused with a degron such that activity of the degron is under control of the sensor. This chapter describes the development of a light-activated, synthetic degron in the model organism Saccharomyces cerevisiae. This photosensitive degron module is composed of the light-oxygen-voltage (LOV) 2 photoreceptor domain of Arabidopsis thaliana phototropin 1 and a degron derived from murine ornithine decarboxylase (ODC). Excitation of the photoreceptor with blue light induces a conformational change that leads to exposure and activation of the degron. Subsequently, the protein is targeted for degradation by the proteasome. Here, the strategy for degron module development and optimization is described in detail together with experimental aspects, which were pivotal for successful implementation of light-controlled proteolysis. The engineering of the photosensitive degron (psd) module may well serve as a blueprint for future development of sophisticated synthetic switches.
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Affiliation(s)
- Christof Taxis
- Department of Biology/Genetics, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany.
- Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany.
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45
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Braguy J, Zurbriggen MD. Synthetic strategies for plant signalling studies: molecular toolbox and orthogonal platforms. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:118-38. [PMID: 27227549 DOI: 10.1111/tpj.13218] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 05/11/2016] [Accepted: 05/13/2016] [Indexed: 05/15/2023]
Abstract
Plants deploy a wide array of signalling networks integrating environmental cues with growth, defence and developmental responses. The high level of complexity, redundancy and connection between several pathways hampers a comprehensive understanding of involved functional and regulatory mechanisms. The implementation of synthetic biology approaches is revolutionizing experimental biology in prokaryotes, yeasts and animal systems and can likewise contribute to a new era in plant biology. This review gives an overview on synthetic biology approaches for the development and implementation of synthetic molecular tools and techniques to interrogate, understand and control signalling events in plants, ranging from strategies for the targeted manipulation of plant genomes up to the spatiotemporally resolved control of gene expression using optogenetic approaches. We also describe strategies based on the partial reconstruction of signalling pathways in orthogonal platforms, like yeast, animal and in vitro systems. This allows a targeted analysis of individual signalling hubs devoid of interconnectivity with endogenous interacting components. Implementation of the interdisciplinary synthetic biology tools and strategies is not exempt of challenges and hardships but simultaneously most rewarding in terms of the advances in basic and applied research. As witnessed in other areas, these original theoretical-experimental avenues will lead to a breakthrough in the ability to study and comprehend plant signalling networks.
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Affiliation(s)
- Justine Braguy
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
- King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, University of Düsseldorf, Universitätstrasse 1, Building 26.12.U1.25, Düsseldorf, 40225, Germany
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46
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Renicke C, Taxis C. Biophotography: concepts, applications and perspectives. Appl Microbiol Biotechnol 2016; 100:3415-20. [PMID: 26887320 DOI: 10.1007/s00253-016-7384-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/03/2016] [Accepted: 02/05/2016] [Indexed: 11/27/2022]
Abstract
Synthetic biology aims at manipulating biological systems by rationally designed and genetically introduced components. Efforts in photoactuator engineering resulted in microorganisms reacting to extracellular light-cues with various cellular responses. Some of them lead to the formation of macroscopically observable outputs, which can be used to generate images made of living matter. Several methods have been developed to convert colorless compounds into visible pigments by an enzymatic conversion. This has been exploited as a showcase for successful creation of an optogenetic tool; examples for basic light-controlled biological processes that have been coupled to this biophotography comprise regulation of transcription, protein stability, and second messenger synthesis. Moreover, biological reproduction of images is used as means to facilitate quantitative characterization of optogenetic switches as well as a technique to investigate complex cellular signaling circuits. Here, we will compare the different techniques for biological image generation, introduce experimental approaches, and provide future-perspectives for biophotography.
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Affiliation(s)
- Christian Renicke
- Department of Biology/Genetics, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Christof Taxis
- Department of Biology/Genetics, Philipps-Universität Marburg, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany. .,Department of Chemistry/Biochemistry, Philipps-Universität Marburg, Hans-Meerwein-Strasse 4, 35043, Marburg, Germany.
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47
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Abstract
Regulation of protein stability is a fundamental process in eukaryotic cells and pivotal to, e.g., cell cycle progression, faithful chromosome segregation, or protein quality control. Synthetic regulation of protein stability requires conditional degradation sequences (degrons) that induce a stability switch upon a specific signal. Fusion to a selected target protein permits to influence virtually every process in a cell. Light as signal is advantageous due to its precise applicability in time, space, quality, and quantity. Light control of protein stability was achieved by fusing the LOV2 photoreceptor domain of Arabidopsis thaliana phototropin1 with a synthetic degron (cODC1) derived from the carboxy-terminal degron of ornithine decarboxylase to obtain the photosensitive degron (psd) module. The psd module can be attached to the carboxy terminus of target proteins that are localized to the cytosol or nucleus to obtain light control over their stability. Blue light induces structural changes in the LOV2 domain, which in turn lead to activation of the degron and thus proteasomal degradation of the whole fusion protein. Variants of the psd module with diverse characteristics are useful to fine-tune the stability of a selected target at permissive (darkness) and restrictive conditions (blue light).
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48
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Beyer HM, Juillot S, Herbst K, Samodelov SL, Müller K, Schamel WW, Römer W, Schäfer E, Nagy F, Strähle U, Weber W, Zurbriggen MD. Red Light-Regulated Reversible Nuclear Localization of Proteins in Mammalian Cells and Zebrafish. ACS Synth Biol 2015; 4:951-8. [PMID: 25803699 DOI: 10.1021/acssynbio.5b00004] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein trafficking in and out of the nucleus represents a key step in controlling cell fate and function. Here we report the development of a red light-inducible and far-red light-reversible synthetic system for controlling nuclear localization of proteins in mammalian cells and zebrafish. First, we synthetically reconstructed and validated the red light-dependent Arabidopsis phytochrome B nuclear import mediated by phytochrome-interacting factor 3 in a nonplant environment and support current hypotheses on the import mechanism in planta. On the basis of this principle we next regulated nuclear import and activity of target proteins by the spatiotemporal projection of light patterns. A synthetic transcription factor was translocated into the nucleus of mammalian cells and zebrafish to drive transgene expression. These data demonstrate the first in vivo application of a plant phytochrome-based optogenetic tool in vertebrates and expand the repertoire of available light-regulated molecular devices.
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Affiliation(s)
- Hannes M. Beyer
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
| | - Samuel Juillot
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
| | - Kathrin Herbst
- Institute
of Toxicology and Genetics, Karlsruhe Institute of Technology and University of Heidelberg, D-76344 Eggenstein-Leopoldshafen, Germany
- BIF-IGS − BioInterfaces International Graduate School, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Sophia L. Samodelov
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
| | - Konrad Müller
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Wolfgang W. Schamel
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
- CCI, Centre
for Chronic Immunodeficiency, University Clinincs Freiburg, Breisacher
Strasse 117, 79106 Freiburg, Germany
| | - Winfried Römer
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
| | - Eberhard Schäfer
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Ferenc Nagy
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- Biological
Research Centre, Institute of Plant Biology, H-6726 Szeged, Hungary
| | - Uwe Strähle
- Institute
of Toxicology and Genetics, Karlsruhe Institute of Technology and University of Heidelberg, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Wilfried Weber
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
- SGBM
− Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstrasse 19a, 79104 Freiburg, Germany
- ZBSA
− Centre for Biosystems Analysis, University of Freiburg, Habsburgerstrasse 49, 79104 Freiburg, Germany
| | - Matias D. Zurbriggen
- Faculty
of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
- BIOSS
− Centre for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
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49
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Castillo-Hair SM, Igoshin OA, Tabor JJ. How to train your microbe: methods for dynamically characterizing gene networks. Curr Opin Microbiol 2015; 24:113-23. [PMID: 25677419 DOI: 10.1016/j.mib.2015.01.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/06/2015] [Accepted: 01/10/2015] [Indexed: 12/31/2022]
Abstract
Gene networks regulate biological processes dynamically. However, researchers have largely relied upon static perturbations, such as growth media variations and gene knockouts, to elucidate gene network structure and function. Thus, much of the regulation on the path from DNA to phenotype remains poorly understood. Recent studies have utilized improved genetic tools, hardware, and computational control strategies to generate precise temporal perturbations outside and inside of live cells. These experiments have, in turn, provided new insights into the organizing principles of biology. Here, we introduce the major classes of dynamical perturbations that can be used to study gene networks, and discuss technologies available for creating them in a wide range of microbial pathways.
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Affiliation(s)
| | - Oleg A Igoshin
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, United States; Department of Biosciences, Rice University, 6100 Main Street, Houston, TX 77005, United States; Center for Theoretical Biophysics, Rice University, 6100 Main Street, Houston, TX 77005, United States
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, 6100 Main Street, Houston, TX 77005, United States; Department of Biosciences, Rice University, 6100 Main Street, Houston, TX 77005, United States.
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