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Ligunas GD, Paniagua GF, LaBelle J, Ramos-Martinez A, Shen K, Gerlt EH, Aguilar K, Nguyen N, Materna SC, Woo S. Tissue-specific and endogenous protein labeling with split fluorescent proteins. Dev Biol 2024; 514:109-116. [PMID: 38908500 DOI: 10.1016/j.ydbio.2024.06.011] [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: 03/03/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
The ability to label proteins by fusion with genetically encoded fluorescent proteins is a powerful tool for understanding dynamic biological processes. However, current approaches for expressing fluorescent protein fusions possess drawbacks, especially at the whole organism level. Expression by transgenesis risks potential overexpression artifacts while fluorescent protein insertion at endogenous loci is technically difficult and, more importantly, does not allow for tissue-specific study of broadly expressed proteins. To overcome these limitations, we have adopted the split fluorescent protein system mNeonGreen21-10/11 (split-mNG2) to achieve tissue-specific and endogenous protein labeling in zebrafish. In our approach, mNG21-10 is expressed under a tissue-specific promoter using standard transgenesis while mNG211 is inserted into protein-coding genes of interest using CRISPR/Cas-directed gene editing. Each mNG2 fragment on its own is not fluorescent, but when co-expressed the fragments self-assemble into a fluorescent complex. Here, we report successful use of split-mNG2 to achieve differential labeling of the cytoskeleton genes tubb4b and krt8 in various tissues. We also demonstrate that by anchoring the mNG21-10 component to specific cellular compartments, the split-mNG2 system can be used to manipulate protein localization. Our approach should be broadly useful for a wide range of applications.
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Affiliation(s)
- Gloria D Ligunas
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA; Quantitative and Systems Biology Graduate Group, University of California, Merced, CA, USA
| | - German F Paniagua
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA
| | - Jesselynn LaBelle
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA; Quantitative and Systems Biology Graduate Group, University of California, Merced, CA, USA
| | - Adela Ramos-Martinez
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA
| | - Kyle Shen
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA
| | - Emma H Gerlt
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA
| | - Kaddy Aguilar
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA
| | - Ngoc Nguyen
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA
| | - Stefan C Materna
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA; Quantitative and Systems Biology Graduate Group, University of California, Merced, CA, USA; Health Sciences Research Institute, University of California, Merced, CA, USA
| | - Stephanie Woo
- Department of Molecular and Cell Biology, University of California, Merced, CA, USA; Quantitative and Systems Biology Graduate Group, University of California, Merced, CA, USA; Health Sciences Research Institute, University of California, Merced, CA, USA.
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2
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Gillespie W, Zhang Y, Ruiz OE, Cerda J, Ortiz-Guzman J, Turner WD, Largoza G, Sherman M, Mosser LE, Fujimoto E, Chien CB, Kwan KM, Arenkiel BR, Devine WP, Wythe JD. Multisite Assembly of Gateway Induced Clones (MAGIC): a flexible cloning toolbox with diverse applications in vertebrate model systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603267. [PMID: 39026881 PMCID: PMC11257631 DOI: 10.1101/2024.07.13.603267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Here we present the Multisite Assembly of Gateway Induced Clones (MAGIC) system, which harnesses site-specific recombination-based cloning via Gateway technology for rapid, modular assembly of between 1 and 3 "Entry" vector components, all into a fourth, standard high copy "Destination" plasmid backbone. The MAGIC toolkit spans a range of in vitro and in vivo uses, from directing tunable gene expression, to driving simultaneous expression of microRNAs and fluorescent reporters, to enabling site-specific recombinase-dependent gene expression. All MAGIC system components are directly compatible with existing multisite gateway Tol2 systems currently used in zebrafish, as well as existing eukaryotic cell culture expression Destination plasmids, and available mammalian lentiviral and adenoviral Destination vectors, allowing rapid cross-species experimentation. Moreover, herein we describe novel vectors with flanking piggyBac transposon elements for stable genomic integration in vitro or in vivo when used with piggyBac transposase. Collectively, the MAGIC system facilitates transgenesis in cultured mammalian cells, electroporated mouse and chick embryos, as well as in injected zebrafish embryos, enabling the rapid generation of innovative DNA constructs for biological research due to a shared, common plasmid platform.
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3
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McNamara HM, Jia BZ, Guyer A, Parot VJ, Dobbs C, Schier AF, Cohen AE, Lord ND. Optogenetic control of Nodal signaling patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.11.588875. [PMID: 38645239 PMCID: PMC11030342 DOI: 10.1101/2024.04.11.588875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
A crucial step in early embryogenesis is the establishment of spatial patterns of signaling activity. Tools to perturb morphogen signals with high resolution in space and time can help reveal how embryonic cells decode these signals to make appropriate fate decisions. Here, we present new optogenetic reagents and an experimental pipeline for creaHng designer Nodal signaling patterns in live zebrafish embryos. Nodal receptors were fused to the light-sensitive heterodimerizing pair Cry2/CIB1N, and the Type II receptor was sequestered to the cytosol. The improved optoNodal2 reagents eliminate dark activity and improve response kinetics, without sacrificing dynamic range. We adapted an ultra-widefield microscopy platform for parallel light patterning in up to 36 embryos and demonstrated precise spatial control over Nodal signaling activity and downstream gene expression. Patterned Nodal activation drove precisely controlled internalization of endodermal precursors. Further, we used patterned illumination to generate synthetic signaling patterns in Nodal signaling mutants, rescuing several characteristic developmental defects. This study establishes an experimental toolkit for systematic exploration of Nodal signaling patterns in live embryos.
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Affiliation(s)
| | - Bill Z. Jia
- Department of Systems Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Alison Guyer
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vicente J. Parot
- Institute for Biological and Medical Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Caleb Dobbs
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Adam E. Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Department of Physics, Harvard University, Cambridge, MA, USA
| | - Nathan D. Lord
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, USA
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4
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Ligunas GD, Paniagua G, LaBelle J, Ramos-Martinez A, Shen K, Gerlt EH, Aguilar K, Nguyen A, Materna SC, Woo S. Tissue-specific and endogenous protein labeling with split fluorescent proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.581822. [PMID: 38464062 PMCID: PMC10925240 DOI: 10.1101/2024.02.28.581822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The ability to label proteins by fusion with genetically encoded fluorescent proteins is a powerful tool for understanding dynamic biological processes. However, current approaches for expressing fluorescent protein fusions possess drawbacks, especially at the whole organism level. Expression by transgenesis risks potential overexpression artifacts while fluorescent protein insertion at endogenous loci is technically difficult and, more importantly, does not allow for tissue-specific study of broadly expressed proteins. To overcome these limitations, we have adopted the split fluorescent protein system mNeonGreen21-10/11 (split-mNG2) to achieve tissue-specific and endogenous protein labeling in zebrafish. In our approach, mNG21-10 is expressed under a tissue-specific promoter using standard transgenesis while mNG211 is inserted into protein-coding genes of interest using CRISPR/Cas-directed gene editing. Each mNG2 fragment on its own is not fluorescent, but when co-expressed the fragments self-assemble into a fluorescent complex. Here, we report successful use of split-mNG2 to achieve differential labeling of the cytoskeleton genes tubb4b and krt8 in various tissues. We also demonstrate that by anchoring the mNG21-10 component to specific cellular compartments, the split-mNG2 system can be used to manipulate protein function. Our approach should be broadly useful for a wide range of applications.
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Affiliation(s)
- Gloria D. Ligunas
- Department of Molecular Cell Biology, University of California, Merced, CA USA
- Quantitative and Systems Biology Graduate Group, University of California, Merced, CA USA
| | - German Paniagua
- Department of Molecular Cell Biology, University of California, Merced, CA USA
| | - Jesselynn LaBelle
- Department of Molecular Cell Biology, University of California, Merced, CA USA
- Quantitative and Systems Biology Graduate Group, University of California, Merced, CA USA
| | | | - Kyle Shen
- Department of Molecular Cell Biology, University of California, Merced, CA USA
| | - Emma H. Gerlt
- Department of Molecular Cell Biology, University of California, Merced, CA USA
| | - Kaddy Aguilar
- Department of Molecular Cell Biology, University of California, Merced, CA USA
| | - Alice Nguyen
- Department of Molecular Cell Biology, University of California, Merced, CA USA
| | - Stefan C. Materna
- Department of Molecular Cell Biology, University of California, Merced, CA USA
- Quantitative and Systems Biology Graduate Group, University of California, Merced, CA USA
- Health Sciences Research Institute, University of California, Merced, CA USA
| | - Stephanie Woo
- Department of Molecular Cell Biology, University of California, Merced, CA USA
- Quantitative and Systems Biology Graduate Group, University of California, Merced, CA USA
- Health Sciences Research Institute, University of California, Merced, CA USA
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5
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Devarajan A. Optically Controlled CRISPR-Cas9 and Cre Recombinase for Spatiotemporal Gene Editing: A Review. ACS Synth Biol 2024; 13:25-44. [PMID: 38134336 DOI: 10.1021/acssynbio.3c00596] [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: 12/24/2023]
Abstract
CRISPR-Cas9 and Cre recombinase, two tools extensively used for genome interrogation, have catalyzed key breakthroughs in our understanding of complex biological processes and diseases. However, the immense complexity of biological systems and off-target effects hinder clinical applications, necessitating the development of platforms to control gene editing over spatial and temporal dimensions. Among the strategies developed for inducible control, light is particularly attractive as it is noninvasive and affords high spatiotemporal resolution. The principles for optical control of Cas9 and Cre recombinase are broadly similar and involve photocaged enzymes and small molecules, engineered split- and single-chain constructs, light-induced expression, and delivery by light-responsive nanocarriers. Few systems enable spatiotemporal control with a high dynamic range without loss of wild-type editing efficiencies. Such systems posit the promise of light-activatable systems in the clinic. While the prospect of clinical applications is palpably exciting, optimization and extensive preclinical validation are warranted. Judicious integration of optically activated CRISPR and Cre, tailored for the desired application, may help to bridge the "bench-to-bedside" gap in therapeutic gene editing.
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Affiliation(s)
- Archit Devarajan
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, Madhya Pradesh, India - 462066
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Fu XX, Zhuo DH, Zhang YJ, Li YF, Liu X, Xing YY, Huang Y, Wang YF, Cheng T, Wang D, Chen SH, Chen YJ, Jiang GN, Lu FI, Feng Y, Huang X, Ma J, Liu W, Bai G, Xu PF. A spatiotemporal barrier formed by Follistatin is required for left-right patterning. Proc Natl Acad Sci U S A 2023; 120:e2219649120. [PMID: 37276408 PMCID: PMC10268237 DOI: 10.1073/pnas.2219649120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/25/2023] [Indexed: 06/07/2023] Open
Abstract
How left-right (LR) asymmetry emerges in a patterning field along the anterior-posterior axis remains an unresolved problem in developmental biology. Left-biased Nodal emanating from the LR organizer propagates from posterior to anterior (PA) and establishes the LR pattern of the whole embryo. However, little is known about the regulatory mechanism of the PA spread of Nodal and its asymmetric activation in the forebrain. Here, we identify bilaterally expressed Follistatin (Fst) as a regulator blocking the propagation of the zebrafish Nodal ortholog Southpaw (Spaw) in the right lateral plate mesoderm (LPM), and restricting Spaw transmission in the left LPM to facilitate the establishment of a robust LR asymmetric Nodal patterning. In addition, Fst inhibits the Activin-Nodal signaling pathway in the forebrain thus preventing Nodal activation prior to the arrival, at a later time, of Spaw emanating from the left LPM. This contributes to the orderly propagation of asymmetric Nodal activation along the PA axis. The LR regulation function of Fst is further confirmed in chick and frog embryos. Overall, our results suggest that a robust LR patterning emerges by counteracting a Fst barrier formed along the PA axis.
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Affiliation(s)
- Xin-Xin Fu
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Ding-Hao Zhuo
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Ying-Jie Zhang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Yun-Fei Li
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Xiang Liu
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Yan-Yi Xing
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorders, Hangzhou310058, China
| | - Ying Huang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Yi-Fan Wang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
- Precision Medicine Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore117599, Singapore
| | - Tao Cheng
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Dan Wang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Si-Han Chen
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou310058, China
- Liangzhu Laboratory, Ministry of Education Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, Hangzhou311121, China
| | - Yi-Jian Chen
- Institute of Cell and Developmental Biology, Zhejiang University School of Life Sciences, Hangzhou310058, China
| | - Guan-Nan Jiang
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Fu-I Lu
- Department of Cell Biology, University of Virginia, Charlottesville, VA 22908
| | - Yu Feng
- Department of Biophysics and Infectious Disease of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Xiao Huang
- Institute of Cell and Developmental Biology, Zhejiang University School of Life Sciences, Hangzhou310058, China
| | - Jun Ma
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
| | - Wei Liu
- Department of Metabolic Medicine, International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu32200, China
| | - Ge Bai
- Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou310058, China
- Liangzhu Laboratory, Ministry of Education Frontier Science Center for Brain Science and Brain-machine Integration, State Key Laboratory of Brain-machine Intelligence, Zhejiang University, Hangzhou311121, China
| | - Peng-Fei Xu
- Women's Hospital and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou310058, China
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7
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LaBelle J, Wyatt T, Woo S. Endodermal cells use contact inhibition of locomotion to achieve uniform cell dispersal during zebrafish gastrulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.01.543209. [PMID: 37333383 PMCID: PMC10274714 DOI: 10.1101/2023.06.01.543209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The endoderm is one of the three primary germ layers that ultimately gives rise to the gastrointestinal and respiratory epithelia and other tissues. In zebrafish and other vertebrates, endodermal cells are initially highly migratory with only transient interactions among one other, but later converge together to form an epithelial sheet. Here, we show that during their early, migratory phase, endodermal cells actively avoid each other through contact inhibition of locomotion (CIL), a characteristic response consisting of 1) actin depolymerization and membrane retraction at the site of contact, 2) preferential actin polymerization along a cell-free edge, and 3) reorientation of migration away from the other cell. We found that this response is dependent on the Rho GTPase RhoA and EphA/ephrin-A signaling - expression of dominant-negative (DN) RhoA or treatment with the EphA inhibitor dasatinib resulted in behaviors consistent with loss of CIL, including increased contact duration times and decreased likelihood of migration reorientation after contact. Computational modeling predicted that CIL is required to achieve the efficient and uniform dispersal characteristic of endodermal cells. Consistent with our model, we found that loss of CIL via DN RhoA expression resulted in irregular clustering of cells within the endoderm. Together, our results suggest that endodermal cells use EphA2- and RhoA-dependent CIL as a cell dispersal and spacing mechanism, demonstrating how local interactions can give rise to tissue-scale patterns.
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Affiliation(s)
- Jesselynn LaBelle
- Quantiative and Systems Biology, University of California, Merced, CA USA
| | - Tom Wyatt
- Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS, Université de Paris, France
| | - Stephanie Woo
- Quantiative and Systems Biology, University of California, Merced, CA USA
- Department of Molecular Cell Biology, University of California, Merced, CA USA
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8
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McNamara HM, Ramm B, Toettcher JE. Synthetic developmental biology: New tools to deconstruct and rebuild developmental systems. Semin Cell Dev Biol 2023; 141:33-42. [PMID: 35484026 PMCID: PMC10332110 DOI: 10.1016/j.semcdb.2022.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/13/2022] [Indexed: 11/16/2022]
Abstract
Technological advances have driven many recent advances in developmental biology. Light sheet imaging can reveal single-cell dynamics in living three-dimensional tissues, whereas single-cell genomic methods open the door to a complete catalogue of cell types and gene expression states. An equally powerful but complementary set of approaches are also becoming available to define development processes from the bottom up. These synthetic approaches aim to reconstruct the minimal developmental patterns, signaling processes, and gene networks that produce the basic set of developmental operations: spatial polarization, morphogen interpretation, tissue movement, and cellular memory. In this review we discuss recent approaches at the intersection of synthetic biology and development, including synthetic circuits to deliver and record signaling stimuli and synthetic reconstitution of pattern formation on multicellular scales.
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Affiliation(s)
- Harold M McNamara
- Lewis Sigler Institute, Princeton University, Princeton, NJ 08544, USA; Department of Physics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Beatrice Ramm
- Department of Physics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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9
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Wang Z, Yan Y, Zhang H. A Single-Component Blue Light-Induced System Based on EL222 in Yarrowia lipolytica. Int J Mol Sci 2022; 23:ijms23116344. [PMID: 35683022 PMCID: PMC9181742 DOI: 10.3390/ijms23116344] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/20/2022] [Accepted: 06/02/2022] [Indexed: 01/27/2023] Open
Abstract
Optogenetics has the advantages of a fast response time, reversibility, and high spatial and temporal resolution, which make it desirable in the metabolic engineering of chassis cells. In this study, a light-induced expression system of Yarrowia lipolytica was constructed, which successfully achieved the synthesis and functional verification of Bleomycin resistance protein (BleoR). The core of the blue light-induced system, the light-responsive element (TF), is constructed based on the blue photosensitive protein EL222 and the transcription activator VP16. The results show that the light-induced sensor based on TF, upstream activation sequence (C120)5, and minimal promoter CYC102 can respond to blue light and initiate the expression of GFPMut3 report gene. With four copies of the responsive promoter and reporter gene assembled, they can produce a 128.5-fold higher fluorescent signal than that under dark conditions after 8 h of induction. The effects of light dose and periodicity on this system were investigated, which proved that the system has good spatial and temporal controllability. On this basis, the light-controlled system was used for the synthesis of BleoR to realize the expression and verification of functional protein. These results demonstrated that this system has the potential for the transcriptional regulation of target genes, construction of large-scale synthetic networks, and overproduction of the desired product.
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10
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McFann SE, Shvartsman SY, Toettcher JE. Putting in the Erk: Growth factor signaling and mesoderm morphogenesis. Curr Top Dev Biol 2022; 149:263-310. [PMID: 35606058 DOI: 10.1016/bs.ctdb.2022.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
It has long been known that FGF signaling contributes to mesoderm formation, a germ layer found in triploblasts that is composed of highly migratory cells that give rise to muscles and to the skeletal structures of vertebrates. FGF signaling activates several pathways in the developing mesoderm, including transient activation of the Erk pathway, which triggers mesodermal fate specification through the induction of the gene brachyury and activates morphogenetic programs that allow mesodermal cells to position themselves in the embryo. In this review, we discuss what is known about the generation and interpretation of transient Erk signaling in mesodermal tissues across species. We focus specifically on mechanisms that translate the level and duration of Erk signaling into cell fate and cell movement instructions and discuss strategies for further interrogating the role that Erk signaling dynamics play in mesodermal gastrulation and morphogenesis.
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Affiliation(s)
- Sarah E McFann
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, United States; Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States
| | - Stanislav Y Shvartsman
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, United States; Department of Molecular Biology, Princeton University, Princeton, NJ, United States; Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, United States
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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11
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Wang Z, Yan Y, Zhang H. Design and Characterization of an Optogenetic System in Pichia pastoris. ACS Synth Biol 2022; 11:297-307. [PMID: 34994189 DOI: 10.1021/acssynbio.1c00422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pichia pastoris (P. pastoris) is the workhorse in the commercial production of many valuable proteins. Traditionally, the regulation of gene expression in P. pastoris is achieved through induction by methanol which is toxic and flammable. The emerging optogenetic technology provides an alternative and cleaner gene regulation method. Based on the photosensitive protein EL222, we designed a novel "one-component" optogenetic system. The highest induction ratio was 79.7-fold under blue light compared to the group under darkness. After switching cells from dark to blue illumination, the system induced expression in just 1 h. Only 2 h after the system was switched back to the darkness from blue illumination, the target gene expression was inactivated 5-fold. The induction intensity of the optogenetic system is positively correlated with the dose and periodicity of blue illumination, and it has good spatial control. These results provide the first credible case of optogenetically induced protein expression in P. pastoris.
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Affiliation(s)
- Zhiqian Wang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, People’s Republic of China
| | - Yunjun Yan
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, People’s Republic of China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, People’s Republic of China
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12
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Baillie JS, Stoyek MR, Quinn TA. Seeing the Light: The Use of Zebrafish for Optogenetic Studies of the Heart. Front Physiol 2021; 12:748570. [PMID: 35002753 PMCID: PMC8733579 DOI: 10.3389/fphys.2021.748570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/19/2021] [Indexed: 11/13/2022] Open
Abstract
Optogenetics, involving the optical measurement and manipulation of cellular activity with genetically encoded light-sensitive proteins ("reporters" and "actuators"), is a powerful experimental technique for probing (patho-)physiological function. Originally developed as a tool for neuroscience, it has now been utilized in cardiac research for over a decade, providing novel insight into the electrophysiology of the healthy and diseased heart. Among the pioneering cardiac applications of optogenetic actuators were studies in zebrafish, which first demonstrated their use for precise spatiotemporal control of cardiac activity. Zebrafish were also adopted early as an experimental model for the use of optogenetic reporters, including genetically encoded voltage- and calcium-sensitive indicators. Beyond optogenetic studies, zebrafish are becoming an increasingly important tool for cardiac research, as they combine many of the advantages of integrative and reduced experimental models. The zebrafish has striking genetic and functional cardiac similarities to that of mammals, its genome is fully sequenced and can be modified using standard techniques, it has been used to recapitulate a variety of cardiac diseases, and it allows for high-throughput investigations. For optogenetic studies, zebrafish provide additional advantages, as the whole zebrafish heart can be visualized and interrogated in vivo in the transparent, externally developing embryo, and the relatively small adult heart allows for in situ cell-specific observation and control not possible in mammals. With the advent of increasingly sophisticated fluorescence imaging approaches and methods for spatially-resolved light stimulation in the heart, the zebrafish represents an experimental model with unrealized potential for cardiac optogenetic studies. In this review we summarize the use of zebrafish for optogenetic investigations in the heart, highlighting their specific advantages and limitations, and their potential for future cardiac research.
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Affiliation(s)
- Jonathan S. Baillie
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
| | - Matthew R. Stoyek
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
| | - T. Alexander Quinn
- Department of Physiology and Biophysics, Dalhousie University, Halifax, NS, Canada
- School of Biomedical Engineering, Dalhousie University, Halifax, NS, Canada
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