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Delhaye L, Moschonas GD, Fijalkowska D, Verhee A, De Sutter D, Van de Steene T, De Meyer M, Grzesik H, Van Moortel L, De Bosscher K, Jacobs T, Eyckerman S. Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics. CELL REPORTS METHODS 2024; 4:100818. [PMID: 38986614 PMCID: PMC11294833 DOI: 10.1016/j.crmeth.2024.100818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 05/15/2024] [Accepted: 06/17/2024] [Indexed: 07/12/2024]
Abstract
Protein-protein interactions play an important biological role in every aspect of cellular homeostasis and functioning. Proximity labeling mass spectrometry-based proteomics overcomes challenges typically associated with other methods and has quickly become the current state of the art in the field. Nevertheless, tight control of proximity-labeling enzymatic activity and expression levels is crucial to accurately identify protein interactors. Here, we leverage a T2A self-cleaving peptide and a non-cleaving mutant to accommodate the protein of interest in the experimental and control TurboID setup. To allow easy and streamlined plasmid assembly, we built a Golden Gate modular cloning system to generate plasmids for transient expression and stable integration. To highlight our T2A Split/link design, we applied it to identify protein interactions of the glucocorticoid receptor and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid and non-structural protein 7 (NSP7) proteins by TurboID proximity labeling. Our results demonstrate that our T2A split/link provides an opportune control that builds upon previously established control requirements in the field.
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Affiliation(s)
- Louis Delhaye
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium; OncoRNALab, Center for Medical Genetics Ghent (CMGG), Ghent University, Ghent, Belgium
| | - George D Moschonas
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Annick Verhee
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Delphine De Sutter
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Tessa Van de Steene
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Margaux De Meyer
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Hanna Grzesik
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Department of Cellular and Molecular Medicine, Faculty of Medicine, KU Leuven, Leuven, Belgium
| | - Laura Van Moortel
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Karolien De Bosscher
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
| | - Thomas Jacobs
- VIB-UGent Center for Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Sven Eyckerman
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium; Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium.
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2
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McGlade EA, Mao J, Stephens KK, Kelleher AM, Maddison LA, Bernhardt ML, DeMayo FJ, Lydon JP, Winuthayanon W. Generation of Oviductal Glycoprotein 1 Cre Mouse Model for the Study of Secretory Epithelial Cells of the Oviduct. Endocrinology 2024; 165:bqae070. [PMID: 38916490 PMCID: PMC11210311 DOI: 10.1210/endocr/bqae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/26/2024]
Abstract
The epithelial cell lining of the oviduct plays an important role in oocyte pickup, sperm migration, preimplantation embryo development, and embryo transport. The oviduct epithelial cell layer comprises ciliated and nonciliated secretory cells. The ciliary function has been shown to support gamete and embryo movement in the oviduct, yet secretory cell function has not been well characterized. Therefore, our goal was to generate a secretory cell-specific Cre recombinase mouse model to study the role of the oviductal secretory cells. A knock-in mouse model, Ovgp1Cre:eGFP, was created by expressing Cre from the endogenous Ovgp1 (oviductal glycoprotein 1) locus, with enhanced green fluorescent protein (eGFP) as a reporter. EGFP signals were strongly detected in the secretory epithelial cells of the oviducts at estrus in adult Ovgp1Cre:eGFP mice. Signals were also detected in the ovarian stroma, uterine stroma, vaginal epithelial cells, epididymal epithelial cells, and elongated spermatids. To validate recombinase activity, progesterone receptor (PGR) expression was ablated using the Ovgp1Cre:eGFP; Pgrf/f mouse model. Surprisingly, the deletion was restricted to the epithelial cells of the uterotubal junction (UTJ) region of Ovgp1Cre:eGFP; Pgrf/f oviducts. Deletion of Pgr in the epithelial cells of the UTJ region had no effect on female fecundity. In summary, we found that eGFP signals were likely specific to secretory epithelial cells in all regions of the oviduct. However, due to a potential target-specific Cre activity, validation of appropriate recombination and expression of the gene(s) of interest is absolutely required to confirm efficient deletion when generating conditional knockout mice using the Ovgp1Cre:eGFP line.
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Affiliation(s)
- Emily A McGlade
- Obstetrics, Gynecology and Women's Health, University of Missouri–Columbia, Columbia, MO 65211, USA
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Jiude Mao
- Obstetrics, Gynecology and Women's Health, University of Missouri–Columbia, Columbia, MO 65211, USA
| | - Kalli K Stephens
- Obstetrics, Gynecology and Women's Health, University of Missouri–Columbia, Columbia, MO 65211, USA
| | - Andrew M Kelleher
- Obstetrics, Gynecology and Women's Health, University of Missouri–Columbia, Columbia, MO 65211, USA
| | - Lisette A Maddison
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Miranda L Bernhardt
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Francesco J DeMayo
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - John P Lydon
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wipawee Winuthayanon
- Obstetrics, Gynecology and Women's Health, University of Missouri–Columbia, Columbia, MO 65211, USA
- Center for Reproductive Biology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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3
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Leblanc J, Boulle O, Roux E, Nicolas J, Lavenier D, Audic Y. Fully in vitro iterative construction of a 24 kb-long artificial DNA sequence to store digital information. Biotechniques 2024; 76:203-215. [PMID: 38573592 DOI: 10.2144/btn-2023-0109] [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] [Indexed: 04/05/2024] Open
Abstract
In the absence of a DNA template, the ab initio production of long double-stranded DNA molecules of predefined sequences is particularly challenging. The DNA synthesis step remains a bottleneck for many applications such as functional assessment of ancestral genes, analysis of alternative splicing or DNA-based data storage. In this report we propose a fully in vitro protocol to generate very long double-stranded DNA molecules starting from commercially available short DNA blocks in less than 3 days using Golden Gate assembly. This innovative application allowed us to streamline the process to produce a 24 kb-long DNA molecule storing part of the Declaration of the Rights of Man and of the Citizen of 1789 . The DNA molecule produced can be readily cloned into a suitable host/vector system for amplification and selection.
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Affiliation(s)
- Julien Leblanc
- University Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, Rennes, France
| | - Olivier Boulle
- University Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, Rennes, France
| | - Emeline Roux
- Institut NuMeCan, INRAE, INSERM, University Rennes, France
| | - Jacques Nicolas
- University Rennes, Inria, CNRS, IRISA, Campus de Beaulieu, Rennes, France
| | | | - Yann Audic
- CNRS, University Rennes, Institut de Génétique et Développement de Rennes (IGDR) UMR 6290, Rennes, France
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García-Paz FDM, Del Moral S, Morales-Arrieta S, Ayala M, Treviño-Quintanilla LG, Olvera-Carranza C. Multidomain chimeric enzymes as a promising alternative for biocatalysts improvement: a minireview. Mol Biol Rep 2024; 51:410. [PMID: 38466518 DOI: 10.1007/s11033-024-09332-9] [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: 10/26/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
Searching for new and better biocatalysts is an area of study in constant development. In nature, mechanisms generally occurring in evolution, such as genetic duplication, recombination, and natural selection processes, produce various enzymes with different architectures and properties. The recombination of genes that code proteins produces multidomain chimeric enzymes that contain two or more domains that sometimes enhance their catalytic properties. Protein engineering has mimicked this process to enhance catalytic activity and the global stability of enzymes, searching for new and better biocatalysts. Here, we present and discuss examples from both natural and synthetic multidomain chimeric enzymes and how additional domains heighten their stability and catalytic activity. Moreover, we also describe progress in developing new biocatalysts using synthetic fusion enzymes and revise some methodological strategies to improve their biological fitness.
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Affiliation(s)
- Flor de María García-Paz
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa CP 62210, Cuernavaca, Morelos, México
| | - Sandra Del Moral
- Investigador por México-CONAHCyT, Unidad de Investigación y Desarrollo en Alimentos, Tecnológico Nacional de México, Campus Veracruz. MA de Quevedo 2779, Col. Formando Hogar, CP 91960, Veracruz, Veracruz, México
| | - Sandra Morales-Arrieta
- Departamento de Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566 Col. Lomas del Texcal CP 62550, Jiutepec, Morelos, México
| | - Marcela Ayala
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa CP 62210, Cuernavaca, Morelos, México
| | - Luis Gerardo Treviño-Quintanilla
- Departamento de Biotecnología, Universidad Politécnica del Estado de Morelos, Boulevard Cuauhnáhuac No. 566 Col. Lomas del Texcal CP 62550, Jiutepec, Morelos, México
| | - Clarita Olvera-Carranza
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Col. Chamilpa CP 62210, Cuernavaca, Morelos, México.
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5
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Piepers M, Erbstein K, Reyes-Hernandez J, Song C, Tessi T, Petrasiunaite V, Faerber N, Distel K, Maizel A. GreenGate 2.0: Backwards compatible addons for assembly of complex transcriptional units and their stacking with GreenGate. PLoS One 2023; 18:e0290097. [PMID: 37682951 PMCID: PMC10490876 DOI: 10.1371/journal.pone.0290097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Molecular cloning is a crucial technique in genetic engineering that enables the precise design of synthetic transcriptional units (TUs) and the manipulation of genomes. GreenGate and several other modular molecular cloning systems were developed about ten years ago and are widely used in plant research. All these systems define grammars for assembling transcriptional units from building blocks, cloned as Level 0 modules flanked by four-base pair overhangs and recognition sites for a particular Type IIs endonuclease. Modules are efficiently assembled into Level 1 TUs in a hierarchical assembly process, and Level 2 multigene constructs are assembled by stacking Level 1 TUs. GreenGate is highly popular but has three main limitations. First, using ad-hoc overhangs added by PCR and classical restriction/ligation prevents the efficient use of a one-pot, one-step reaction to generate entry clones and domesticate internal sites; second, a Level 1 TU is assembled from a maximum of six modules, which may be limiting for applications such as multiplex genome editing; third, the generation of Level 2 assemblies is sequential and inefficient. GreenGate 2.0 (GG2.0) expands GreenGate features. It introduces additional overhangs, allowing for the combination of up to 12 Level 0 modules in a Level 1 TU. It includes a Universal Entry Generator plasmid (pUEG) to streamline the generation of Level 0 modules. GG2.0 introduces GreenBraid, a convenient method for stacking transcriptional units iteratively for multigene assemblies. Importantly, GG2.0 is backwards compatible with most existing GreenGate modules. Additionally, GG2.0 includes Level 0 modules for multiplex expression of guide RNAs for CRISPR/Cas9 genome editing and pre-assembled Level 1 vectors for dexamethasone-inducible gene expression and ubiquitous expression of plasma membrane and nuclear fluorescent markers. GG2.0 streamlines and increases the versatility of assembling complex transcriptional units and their combination.
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Affiliation(s)
- Marcel Piepers
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Katarina Erbstein
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | | | - Changzheng Song
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Tomas Tessi
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Vesta Petrasiunaite
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Naja Faerber
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Kathrin Distel
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
| | - Alexis Maizel
- Center for Organismal Studies (COS), University of Heidelberg, Heidelberg, Germany
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Dewaele S, Delhaye L, De Paepe B, Bogaert B, Martinez R, Anckaert J, Yigit N, Nuytens J, Van Coster R, Eyckerman S, Raemdonck K, Mestdagh P. mTOR Inhibition Enhances Delivery and Activity of Antisense Oligonucleotides in Uveal Melanoma Cells. Nucleic Acid Ther 2023; 33:248-264. [PMID: 37389884 DOI: 10.1089/nat.2023.0008] [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] [Indexed: 07/01/2023] Open
Abstract
Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Owing to a lack of effective treatments, patients with metastatic disease have a median survival time of 6-12 months. We recently demonstrated that the Survival Associated Mitochondrial Melanoma Specific Oncogenic Non-coding RNA (SAMMSON) is essential for UM cell survival and that antisense oligonucleotide (ASO)-mediated silencing of SAMMSON impaired cell viability and tumor growth in vitro and in vivo. By screening a library of 2911 clinical stage compounds, we identified the mammalian target of rapamycin (mTOR) inhibitor GDC-0349 to synergize with SAMMSON inhibition in UM. Mechanistic studies revealed that mTOR inhibition enhanced uptake and reduced lysosomal accumulation of lipid complexed SAMMSON ASOs, improving SAMMSON knockdown and further decreasing UM cell viability. We found mTOR inhibition to also enhance target knockdown in other cancer cell lines as well as normal cells when combined with lipid nanoparticle complexed or encapsulated ASOs or small interfering RNAs (siRNAs). Our results are relevant to nucleic acid treatment in general and highlight the potential of mTOR inhibition to enhance ASO and siRNA-mediated target knockdown.
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Affiliation(s)
- Shanna Dewaele
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Louis Delhaye
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
| | - Boel De Paepe
- Division of Pediatric Neurology and Metabolism, Department of Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Bram Bogaert
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Laboratory for General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - Ramiro Martinez
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jasper Anckaert
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nurten Yigit
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Justine Nuytens
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Rudy Van Coster
- Division of Pediatric Neurology and Metabolism, Department of Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Sven Eyckerman
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Biotechnology, VIB-Ghent University, Ghent, Belgium
| | - Koen Raemdonck
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Laboratory for General Biochemistry and Physical Pharmacy, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Center for Medical Genetics (CMGG), Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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7
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Medert R, Thumberger T, Tavhelidse-Suck T, Hub T, Kellner T, Oguchi Y, Dlugosz S, Zimmermann F, Wittbrodt J, Freichel M. Efficient single copy integration via homology-directed repair (scHDR) by 5'modification of large DNA donor fragments in mice. Nucleic Acids Res 2023; 51:e14. [PMID: 36533445 PMCID: PMC10021492 DOI: 10.1093/nar/gkac1150] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 09/22/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
CRISPR/Cas-based approaches have largely replaced conventional gene targeting strategies. However, homology-directed repair (HDR) in the mouse genome is not very efficient, and precisely inserting longer sequences using HDR remains challenging given that donor constructs preferentially integrate as concatemers. Here, we showed that injecting 5' biotinylated donor DNA into mouse embryos at the two-cell stage led to efficient single-copy HDR (scHDR) allele generation. Our dedicated genotyping strategy showed that these alleles occurred with frequencies of 19%, 20%, and 26% at three independent gene loci, indicating that scHDR was dramatically increased by 5' biotinylation. Thus, we suggest that the combination of a 5' biotinylated donor and diligent analysis of concatemer integration are prerequisites for efficiently and reliably generating conditional alleles or other large fragment knock-ins in the mouse genome.
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Affiliation(s)
- Rebekka Medert
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Tobias Hub
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yoko Oguchi
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Sascha Dlugosz
- Interfacultary Biomedical Faculty (IBF), Heidelberg University, Heidelberg, Germany
| | - Frank Zimmermann
- Interfacultary Biomedical Faculty (IBF), Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg, Germany
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8
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Zmuda AJ, Niehaus TD. Systems and strategies for plant protein expression. Methods Enzymol 2023; 680:3-34. [PMID: 36710015 DOI: 10.1016/bs.mie.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
At least a quarter of the protein-encoding genes in plant genomes are predicted to encode enzymes for which no physiological function is known. Determining functions for these uncharacterized enzymes is key to understanding plant metabolism. Functional characterization typically requires expression and purification of recombinant enzymes to be used in enzyme assays and/or for protein structure elucidation studies. Here, we describe several practical considerations used to improve the heterologous expression and purification of Arabidopsis thaliana and Zea mays NAD(P)HX dehydratase (NAXD) and NAD(P)HX epimerase (NAXE), two enzymes that are involved in repair of chemically damaged NAD(P)H cofactors. We provide protocols for transit peptide prediction and construct design, expression in Escherichia coli, and purification of NAXD and NAXE. Many of these strategies are generally applicable to the purification of any plant protein.
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Affiliation(s)
- Anthony J Zmuda
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States
| | - Thomas D Niehaus
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States.
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9
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Ferigolo LF, Vicente MH, Nogueira FT. Brick into the Gateway (BiG): A novel approach for faster cloning combining Golden Gate and Gateway methods. Plasmid 2022; 121:102630. [DOI: 10.1016/j.plasmid.2022.102630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/29/2022] [Accepted: 04/05/2022] [Indexed: 11/26/2022]
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10
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Thumberger T, Tavhelidse-Suck T, Gutierrez-Triana JA, Cornean A, Medert R, Welz B, Freichel M, Wittbrodt J. Boosting targeted genome editing using the hei-tag. eLife 2022; 11:70558. [PMID: 35333175 PMCID: PMC9068219 DOI: 10.7554/elife.70558] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
Precise, targeted genome editing by CRISPR/Cas9 is key for basic research and translational approaches in model and non-model systems. While active in all species tested so far, editing efficiencies still leave room for improvement. The bacterial Cas9 needs to be efficiently shuttled into the nucleus as attempted by fusion with nuclear localization signals (NLSs). Additional peptide tags such as FLAG- or myc-tags are usually added for immediate detection or straightforward purification. Immediate activity is usually granted by administration of preassembled protein/RNA complexes. We present the ‘hei-tag (high efficiency-tag)’ which boosts the activity of CRISPR/Cas genome editing tools already when supplied as mRNA. The addition of the hei-tag, a myc-tag coupled to an optimized NLS via a flexible linker, to Cas9 or a C-to-T (cytosine-to-thymine) base editor dramatically enhances the respective targeting efficiency. This results in an increase in bi-allelic editing, yet reduction of allele variance, indicating an immediate activity even at early developmental stages. The hei-tag boost is active in model systems ranging from fish to mammals, including tissue culture applications. The simple addition of the hei-tag allows to instantly upgrade existing and potentially highly adapted systems as well as to establish novel highly efficient tools immediately applicable at the mRNA level. The genetic code stored within DNA provides cells with the instructions they need to carry out their role in the body. Any changes to these genes, or the DNA sequence around them, has the potential to completely alter how a cell behaves. Scientists have developed various tools that allow them to experimentally modify the genome of cells or even entire living organisms. This includes the popular Cas9 enzyme which cuts DNA at specific sites, and base editors which can precisely change bits of genetic code without cutting DNA. While there are lots of Cas9 enzymes and base editors currently available, these often differ greatly in their activity depending on which cell type or organism they are applied to. Finding a tool that can effectively modify the genome of an organism at the right time during development also poses a challenge. All the cells in an organism arise from a single fertilized cell. If this cell is genetically edited, all its subsequent daughter cells (which make up the entire organism) will contain the genetic modification. However, most genome editing tools only work efficiently later in development, resulting in an undesirable mosaic organism composed of both edited and non-edited cells. Here, Thumberger et al. have developed a new ‘high efficiency-tag’ (also known as hei-tag for short) that can enhance the activity of gene editing tools and overcome this barrier. The tag improves the efficiency of gene editing by immediately shuttling a Cas9 enzyme to the nucleus, the cellular compartment that stores DNA. In all cases, gene editing tools with hei-tag worked better than those without in fish embryos and mouse cells grown in the laboratory. When Cas9 enzymes connected to a hei-tag were injected into the first fertilized cell of a fish embryo, this resulted in an even distribution of edited genes spread throughout the whole organism. To understand how a gene affects an organism, researchers need to be able to edit it as early in development as possible. Attaching the ‘hei-tag’ to already available tools could help boost their activity and make them more efficient. It could also allow advances in medical research aimed at replacing faulty genes with fully functioning ones.
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Affiliation(s)
- Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | | | - Alex Cornean
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Rebekka Medert
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Bettina Welz
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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11
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Kramme C, Plesa AM, Wang HH, Wolf B, Smela MP, Guo X, Kohman RE, Chatterjee P, Church GM. An integrated pipeline for mammalian genetic screening. CELL REPORTS METHODS 2021; 1:100082. [PMID: 35474898 PMCID: PMC9017118 DOI: 10.1016/j.crmeth.2021.100082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022]
Abstract
With the recent advancements in genome editing, next-generation sequencing (NGS), and scalable cloning techniques, scientists can now conduct genetic screens at unprecedented levels of scale and precision. With such a multitude of technologies, there is a need for a simple yet comprehensive pipeline to enable systematic mammalian genetic screening. In this study, we develop unique algorithms for target identification and a toxin-less Gateway cloning tool, termed MegaGate, for library cloning which, when combined with existing genetic perturbation methods and NGS-coupled readouts, enable versatile engineering of relevant mammalian cell lines. Our integrated pipeline for sequencing-based target ascertainment and modular perturbation screening (STAMPScreen) can thus be utilized for a host of cell state engineering applications.
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Affiliation(s)
- Christian Kramme
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Alexandru M. Plesa
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Helen H. Wang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Bennett Wolf
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Merrick Pierson Smela
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Xiaoge Guo
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Richie E. Kohman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Pranam Chatterjee
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
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12
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PARylation prevents the proteasomal degradation of topoisomerase I DNA-protein crosslinks and induces their deubiquitylation. Nat Commun 2021; 12:5010. [PMID: 34408146 PMCID: PMC8373905 DOI: 10.1038/s41467-021-25252-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/22/2021] [Indexed: 11/08/2022] Open
Abstract
Poly(ADP)-ribosylation (PARylation) regulates chromatin structure and recruits DNA repair proteins. Using single-molecule fluorescence microscopy to track topoisomerase I (TOP1) in live cells, we found that sustained PARylation blocked the repair of TOP1 DNA-protein crosslinks (TOP1-DPCs) in a similar fashion as inhibition of the ubiquitin-proteasome system (UPS). PARylation of TOP1-DPC was readily revealed by inhibiting poly(ADP-ribose) glycohydrolase (PARG), indicating the otherwise transient and reversible PARylation of the DPCs. As the UPS is a key repair mechanism for TOP1-DPCs, we investigated the impact of TOP1-DPC PARylation on the proteasome and found that the proteasome is unable to associate with and digest PARylated TOP1-DPCs. In addition, PARylation recruits the deubiquitylating enzyme USP7 to reverse the ubiquitylation of PARylated TOP1-DPCs. Our work identifies PARG as repair factor for TOP1-DPCs by enabling the proteasomal digestion of TOP1-DPCs. It also suggests the potential regulatory role of PARylation for the repair of a broad range of DPCs.
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13
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Zilova L, Weinhardt V, Tavhelidse T, Schlagheck C, Thumberger T, Wittbrodt J. Fish primary embryonic pluripotent cells assemble into retinal tissue mirroring in vivo early eye development. eLife 2021; 10:e66998. [PMID: 34252023 PMCID: PMC8275126 DOI: 10.7554/elife.66998] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Organoids derived from pluripotent stem cells promise the solution to current challenges in basic and biomedical research. Mammalian organoids are however limited by long developmental time, variable success, and lack of direct comparison to an in vivo reference. To overcome these limitations and address species-specific cellular organization, we derived organoids from rapidly developing teleosts. We demonstrate how primary embryonic pluripotent cells from medaka and zebrafish efficiently assemble into anterior neural structures, particularly retina. Within 4 days, blastula-stage cell aggregates reproducibly execute key steps of eye development: retinal specification, morphogenesis, and differentiation. The number of aggregated cells and genetic factors crucially impacted upon the concomitant morphological changes that were intriguingly reflecting the in vivo situation. High efficiency and rapid development of fish-derived organoids in combination with advanced genome editing techniques immediately allow addressing aspects of development and disease, and systematic probing of impact of the physical environment on morphogenesis and differentiation.
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Affiliation(s)
- Lucie Zilova
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Venera Weinhardt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Christina Schlagheck
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
- Heidelberg International Biosciences Graduate School HBIGS and HeiKa Graduate School on “Functional Materials”HeidelbergGermany
| | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
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14
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Quillien A, Gilbert G, Boulet M, Ethuin S, Waltzer L, Vandel L. Prmt5 promotes vascular morphogenesis independently of its methyltransferase activity. PLoS Genet 2021; 17:e1009641. [PMID: 34153034 PMCID: PMC8248709 DOI: 10.1371/journal.pgen.1009641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 07/01/2021] [Accepted: 06/02/2021] [Indexed: 01/02/2023] Open
Abstract
During development, the vertebrate vasculature undergoes major growth and remodeling. While the transcriptional cascade underlying blood vessel formation starts to be better characterized, little is known concerning the role and mode of action of epigenetic enzymes during this process. Here, we explored the role of the Protein Arginine Methyl Transferase Prmt5 in blood vessel formation as well as hematopoiesis using zebrafish as a model system. Through the combination of different prmt5 loss-of-function approaches we highlighted a key role of Prmt5 in both processes. Notably, we showed that Prmt5 promotes vascular morphogenesis through the transcriptional control of ETS transcription factors and adhesion proteins in endothelial cells. Interestingly, using a catalytic dead mutant of Prmt5 and a specific drug inhibitor, we found that while Prmt5 methyltransferase activity was required for blood cell formation, it was dispensable for vessel formation. Analyses of chromatin architecture impact on reporter genes expression and chromatin immunoprecipitation experiments led us to propose that Prmt5 regulates transcription by acting as a scaffold protein that facilitates chromatin looping to promote vascular morphogenesis. Blood vessel formation is an essential developmental process required for the survival of all vertebrates. The vascular anatomy and the mechanisms involved in vessel formation are highly conserved among vertebrates. Hence, we used zebrafish as a model, to decipher the role and the mode of action of Prmt5, an enzyme known to regulate gene expression, in vascular morphogenesis and in blood cell formation in vivo. Using different approaches, we highlighted a key role of Prmt5 during both processes. However, we found that while blood cell formation required Prmt5 enzymatic activity, vascular morphogenesis was independent on its activity. Prmt5 has been proposed as a therapeutic target in many diseases, including cancer. Yet, we show here that Prmt5 acts at least in part independently of its methyltransferase activity to regulate vascular morphogenesis. By shedding light on a mechanism of action of Prmt5 that will be insensitive to enzymatic inhibitors, our data calls forth the design of alternative drugs. In addition, this non-canonical function of Prmt5 may have a more pervasive role than previously thought in physiological conditions, i.e. during development, but also in pathological situations such as in tumor angiogenesis and certainly deserves more attention in the future.
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Affiliation(s)
- Aurélie Quillien
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- RESTORE, INSERM UMR1301, CNRS UMR5070, Université Paul Sabatier, Université de Toulouse, Toulouse, France
- * E-mail: (AQ); (LV)
| | - Guerric Gilbert
- Université Clermont Auvergne, CNRS, INSERM, iGReD, Clermont-Ferrand, France
| | - Manon Boulet
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- Université Clermont Auvergne, CNRS, INSERM, iGReD, Clermont-Ferrand, France
| | - Séverine Ethuin
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lucas Waltzer
- Université Clermont Auvergne, CNRS, INSERM, iGReD, Clermont-Ferrand, France
| | - Laurence Vandel
- Centre de Biologie du Développement (CBD), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
- Université Clermont Auvergne, CNRS, INSERM, iGReD, Clermont-Ferrand, France
- * E-mail: (AQ); (LV)
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15
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Kölsch Y, Hahn J, Sappington A, Stemmer M, Fernandes AM, Helmbrecht TO, Lele S, Butrus S, Laurell E, Arnold-Ammer I, Shekhar K, Sanes JR, Baier H. Molecular classification of zebrafish retinal ganglion cells links genes to cell types to behavior. Neuron 2021; 109:645-662.e9. [PMID: 33357413 PMCID: PMC7897282 DOI: 10.1016/j.neuron.2020.12.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/09/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022]
Abstract
Retinal ganglion cells (RGCs) form an array of feature detectors, which convey visual information to central brain regions. Characterizing RGC diversity is required to understand the logic of the underlying functional segregation. Using single-cell transcriptomics, we systematically classified RGCs in adult and larval zebrafish, thereby identifying marker genes for >30 mature types and several developmental intermediates. We used this dataset to engineer transgenic driver lines, enabling specific experimental access to a subset of RGC types. Expression of one or few transcription factors often predicts dendrite morphologies and axonal projections to specific tectal layers and extratectal targets. In vivo calcium imaging revealed that molecularly defined RGCs exhibit specific functional tuning. Finally, chemogenetic ablation of eomesa+ RGCs, which comprise melanopsin-expressing types with projections to a small subset of central targets, selectively impaired phototaxis. Together, our study establishes a framework for systematically studying the functional architecture of the visual system.
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Affiliation(s)
- Yvonne Kölsch
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany; Graduate School of Systemic Neurosciences, Ludwig Maximilian University, 82152 Martinsried, Germany
| | - Joshua Hahn
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, CA 94720, USA
| | - Anna Sappington
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Manuel Stemmer
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - António M Fernandes
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Thomas O Helmbrecht
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Shriya Lele
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, CA 94720, USA
| | - Eva Laurell
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Irene Arnold-Ammer
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany
| | - Karthik Shekhar
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, California Institute for Quantitative Biosciences, QB3, Center for Computational Biology, UC Berkeley, Berkeley, CA 94720, USA.
| | - Joshua R Sanes
- Center for Brain Science and Department of Molecular and Cell Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Herwig Baier
- Max Planck Institute of Neurobiology, Department Genes - Circuits - Behavior, 82152 Martinsried, Germany.
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16
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Di Blasi R, Zouein A, Ellis T, Ceroni F. Genetic Toolkits to Design and Build Mammalian Synthetic Systems. Trends Biotechnol 2021; 39:1004-1018. [PMID: 33526300 DOI: 10.1016/j.tibtech.2020.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 11/17/2022]
Abstract
Construction of DNA-encoded programs is central to synthetic biology and the chosen method often determines the time required to design and build constructs for testing. Here, we describe and summarise key features of the available toolkits for DNA construction for mammalian cells. We compare the different cloning strategies based on their complexity and the time needed to generate constructs of different sizes, and we reflect on why Golden Gate toolkits now dominate due to their modular design. We look forward to future advances, including accessory packs for cloning toolkits that can facilitate editing, orthogonality, advanced regulation, and integration into synthetic chromosome construction.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK
| | - Annalise Zouein
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK; Department of Bioengineering, Imperial College London, South Kensington Campus, London, UK
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK; Department of Bioengineering, Imperial College London, South Kensington Campus, London, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Francesca Ceroni
- Department of Chemical Engineering, Imperial College London, South Kensington Campus, London, UK; Imperial College Centre for Synthetic Biology, South Kensington Campus, London, UK.
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17
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Karimi M, Jacobs TB. GoldenGateway: A DNA Assembly Method for Plant Biotechnology. TRENDS IN PLANT SCIENCE 2021; 26:95-96. [PMID: 33158740 DOI: 10.1016/j.tplants.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/13/2020] [Indexed: 05/26/2023]
Affiliation(s)
- Mansour Karimi
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Thomas B Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
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18
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Li J, Li Y, Pawlik KM, Napierala JS, Napierala M. A CRISPR-Cas9, Cre- lox, and Flp- FRT Cascade Strategy for the Precise and Efficient Integration of Exogenous DNA into Cellular Genomes. CRISPR J 2020; 3:470-486. [PMID: 33146562 DOI: 10.1089/crispr.2020.0042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We describe a protocol for the precise integration of exogenous DNA into user-defined genomic loci in cultured cells. This strategy first introduces a promoter and a lox site to a specific location via a Cas9-induced double-strand break. Second, a gene of interest (GOI) is inserted into the lox site via Cre-lox recombination. Upon correct insertion, a cis-linked antibiotic resistance gene will be expressed from a promoter introduced into the genome in the first step assuring selection for correct integrants. Last, the selection cassette is excised via a Flp-FRT recombination event, leaving a precisely targeted GOI. This method is broadly applicable to any exogenous DNA to be integrated, choice of integration site, and choice of cell type. The most remarkable aspect of this versatile approach, termed "CasPi" (cascaded precise integration), is that it allows for precise genome targeting with large, frequently complex, and repetitive DNA sequences that do not integrate efficiently or at all with current genome targeting methods.
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Affiliation(s)
- Jixue Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Yanjie Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Kevin M Pawlik
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jill S Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Marek Napierala
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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19
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Marquez J, Criscione J, Charney RM, Prasad MS, Hwang WY, Mis EK, García-Castro MI, Khokha MK. Disrupted ER membrane protein complex-mediated topogenesis drives congenital neural crest defects. J Clin Invest 2020; 130:813-826. [PMID: 31904590 DOI: 10.1172/jci129308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 10/22/2019] [Indexed: 12/20/2022] Open
Abstract
Multipass membrane proteins have a myriad of functions, including transduction of cell-cell signals, ion transport, and photoreception. Insertion of these proteins into the membrane depends on the endoplasmic reticulum (ER) membrane protein complex (EMC). Recently, birth defects have been observed in patients with variants in the gene encoding a member of this complex, EMC1. Patient phenotypes include congenital heart disease, craniofacial malformations, and neurodevelopmental disease. However, a molecular connection between EMC1 and these birth defects is lacking. Using Xenopus, we identified defects in neural crest cells (NCCs) upon emc1 depletion. We then used unbiased proteomics and discovered a critical role for emc1 in WNT signaling. Consistent with this, readouts of WNT signaling and Frizzled (Fzd) levels were reduced in emc1-depleted embryos, while NCC defects could be rescued with β-catenin. Interestingly, other transmembrane proteins were mislocalized upon emc1 depletion, providing insight into additional patient phenotypes. To translate our findings back to humans, we found that EMC1 was necessary for human NCC development in vitro. Finally, we tested patient variants in our Xenopus model and found the majority to be loss-of-function alleles. Our findings define molecular mechanisms whereby EMC1 dysfunction causes disease phenotypes through dysfunctional multipass membrane protein topogenesis.
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Affiliation(s)
- Jonathan Marquez
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - June Criscione
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Rebekah M Charney
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California, USA
| | - Maneeshi S Prasad
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California, USA
| | - Woong Y Hwang
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Emily K Mis
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Martín I García-Castro
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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20
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Pryor JM, Potapov V, Kucera RB, Bilotti K, Cantor EJ, Lohman GJS. Enabling one-pot Golden Gate assemblies of unprecedented complexity using data-optimized assembly design. PLoS One 2020; 15:e0238592. [PMID: 32877448 PMCID: PMC7467295 DOI: 10.1371/journal.pone.0238592] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/19/2020] [Indexed: 12/21/2022] Open
Abstract
DNA assembly is an integral part of modern synthetic biology, as intricate genetic engineering projects require robust molecular cloning workflows. Golden Gate assembly is a frequently employed DNA assembly methodology that utilizes a Type IIS restriction enzyme and a DNA ligase to generate recombinant DNA constructs from smaller DNA fragments. However, the utility of this methodology has been limited by a lack of resources to guide experimental design. For example, selection of the DNA sequences at fusion sites between fragments is based on broad assembly guidelines or pre-vetted sets of junctions, rather than being customized for a particular application or cloning project. To facilitate the design of robust assembly reactions, we developed a high-throughput DNA sequencing assay to examine reaction outcomes of Golden Gate assembly with T4 DNA ligase and the most commonly used Type IIS restriction enzymes that generate three-base and four-base overhangs. Next, we incorporated these findings into a suite of webtools that design assembly reactions using the experimental data. These webtools can be used to create customized assemblies from a target DNA sequence or a desired number of fragments. Lastly, we demonstrate how using these tools expands the limits of current assembly systems by carrying out one-pot assemblies of up to 35 DNA fragments. Full implementation of the tools developed here enables direct expansion of existing assembly standards for modular cloning systems (e.g. MoClo) as well as the formation of robust new high-fidelity standards.
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Affiliation(s)
- John M. Pryor
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Vladimir Potapov
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Rebecca B. Kucera
- Applications and Product Development, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Katharina Bilotti
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Eric J. Cantor
- Applications and Product Development, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Gregory J. S. Lohman
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
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21
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Liu R, Du K, Ormanns J, Adolfi MC, Schartl M. Melanocortin 4 receptor signaling and puberty onset regulation in Xiphophorus swordtails. Gen Comp Endocrinol 2020; 295:113521. [PMID: 32470471 DOI: 10.1016/j.ygcen.2020.113521] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/15/2020] [Accepted: 05/22/2020] [Indexed: 01/01/2023]
Abstract
Fish of the genus Xiphophorus provide a prominent example of genetic control of male body size and reproductive tactics. In X.nigrensis and X.multilineatus, puberty onset and body length are determined by melanocortin 4 receptor (Mc4r) allelic and copy number variations which were proposed to fine-tune the signaling output of the system. Accessory protein Mrap2 is required for growth across species by affecting Mc4r signaling. The molecular mechanism how Mc4r signaling controls puberty regulation in Xiphophorus and whether the interaction with Mrap2 is also involved was so far unclear. Hence, we examined Mc4r and Mrap2 in X.nigrensis and X.multilineatus, in comparison to a more distantly related species, X.hellerii. mc4r and mrap2 transcripts co-localized in the hypothalamus and preoptic regions in large males, small males and females of X.nigrensis, with similar signal strength for mrap2 but higher expression of mc4r in large males. This overexpression is constituted by wild-type and one subtype of mutant alleles. In vitro studies revealed that Mrap2 co-expressed with Mc4r increased cAMP production but did not change EC50. Cells co-expressing the wild-type and one mutant allele showed lower cAMP signaling than Mc4r wild-type cells. This indicates a role of Mc4r alleles, but not Mrap2, in puberty signaling. Different from X.nigrensis and X.multilineatus, X.hellerii has only wild-type alleles, but also shows a puberty onset and body length polymorphism, despite the absence of mutant alleles. Like in the two other species, mc4r and mrap2 transcripts colocalized and mc4r is expressed at substantially higher levels in large males. This demonstrates that puberty and growth regulation mechanism may not be identical even within same genus.
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MESH Headings
- Adaptor Proteins, Signal Transducing/metabolism
- Alleles
- Amino Acid Sequence
- Animals
- Cyprinodontiformes/genetics
- Cyprinodontiformes/metabolism
- DNA Copy Number Variations/genetics
- Female
- Gene Expression Regulation, Developmental
- Male
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptor, Melanocortin, Type 4/chemistry
- Receptor, Melanocortin, Type 4/genetics
- Receptor, Melanocortin, Type 4/metabolism
- Sexual Maturation/physiology
- Signal Transduction
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Affiliation(s)
- Ruiqi Liu
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Kang Du
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Jenny Ormanns
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Mateus C Adolfi
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Manfred Schartl
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany; The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, USA.
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22
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Bidan N, Bailleul-Dubois J, Duval J, Winter M, Denoulet M, Hannebicque K, El-Sayed IY, Ginestier C, Forissier V, Charafe-Jauffret E, Macario M, Matsunaga YT, Meignan S, Anquez F, Julien S, Bonnefond A, Derhourhi M, Le Bourhis X, Lagadec C. Transcriptomic Analysis of Breast Cancer Stem Cells and Development of a pALDH1A1:mNeptune Reporter System for Live Tracking. Proteomics 2019; 19:e1800454. [PMID: 31430054 DOI: 10.1002/pmic.201800454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 08/12/2019] [Indexed: 12/24/2022]
Abstract
Many solid cancers are hierarchically organized with a small number of cancer stem cells (CSCs) able to regrow a tumor, while their progeny lacks this feature. Breast CSC is known to contribute to therapy resistance. The study of those cells is usually based on their cell-surface markers like CD44high /CD24low/neg or their aldehyde dehydrogenase (ALDH) activity. However, these markers cannot be used to track the dynamics of CSC. Here, a transcriptomic analysis is performed to identify segregating gene expression in CSCs and non-CSCs, sorted by Aldefluor assay. It is observed that among ALDH-associated genes, only ALDH1A1 isoform is increased in CSCs. A CSC reporter system is then developed by using a far red-fluorescent protein (mNeptune) under the control of ALDH1A1 promoter. mNeptune-positive cells exhibit higher sphere-forming capacity, tumor formation, and increased resistance to anticancer therapies. These results indicate that the reporter identifies cells with stemness characteristics. Moreover, live tracking of cells in a microfluidic system reveals a higher extravasation potential of CSCs. Live tracking of non-CSCs under irradiation treatment show, for the first time, live reprogramming of non-CSCs into CSCs. Therefore, the reporter will allow for cell tracking to better understand the implication of CSCs in breast cancer development and recurrence.
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Affiliation(s)
- Nadège Bidan
- University of Lille, U908-CPAC, Cell Plasticity and Cancer, F-59000, Lille, France.,Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France
| | - Justine Bailleul-Dubois
- University of Lille, U908-CPAC, Cell Plasticity and Cancer, F-59000, Lille, France.,Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France.,Institut pour la Recherche sur le Cancer de Lille (IRCL), 59000, Lille, France
| | - Jérémy Duval
- Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France
| | - Marie Winter
- University of Lille, U908-CPAC, Cell Plasticity and Cancer, F-59000, Lille, France.,Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France
| | - Marie Denoulet
- University of Lille, U908-CPAC, Cell Plasticity and Cancer, F-59000, Lille, France.,Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France
| | - Karine Hannebicque
- Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France.,Tumorigenesis and Resistance to Treatment Unit, Centre Oscar Lambret, 3 rue Frédéric Combemale, 59000, Lille, France
| | - Ihsan Y El-Sayed
- University of Lille, U908-CPAC, Cell Plasticity and Cancer, F-59000, Lille, France
| | - Christophe Ginestier
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la recherche Médicale (INSERM) Paoli-Calmettes Institute, Centre de Recherche en Cancérologie de Marseille (CRCM), Epithelial Stem Cells and Cancer Team, University of Aix-Marseille, 13009, Marseille, France
| | - Violaine Forissier
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la recherche Médicale (INSERM) Paoli-Calmettes Institute, Centre de Recherche en Cancérologie de Marseille (CRCM), Epithelial Stem Cells and Cancer Team, University of Aix-Marseille, 13009, Marseille, France
| | - Emmanuelle Charafe-Jauffret
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la recherche Médicale (INSERM) Paoli-Calmettes Institute, Centre de Recherche en Cancérologie de Marseille (CRCM), Epithelial Stem Cells and Cancer Team, University of Aix-Marseille, 13009, Marseille, France
| | - Manon Macario
- Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la recherche Médicale (INSERM) Paoli-Calmettes Institute, Centre de Recherche en Cancérologie de Marseille (CRCM), Epithelial Stem Cells and Cancer Team, University of Aix-Marseille, 13009, Marseille, France
| | - Yukiko T Matsunaga
- Center for International Research on Integrative Biomedical Systems (CIBiS), Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.,LIMMS/CNRS-IIS (UMI 2820), Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan.,Centre National de la Recherche Scientifique (CNRS)/IIS/COL/Lille University SMMiL-E Project, CNRS Délégation Nord-Pas de Calais et Picardie, 2 rue de Canonniers, Lille, Cedex, 59046, France
| | - Samuel Meignan
- Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France.,Institut pour la Recherche sur le Cancer de Lille (IRCL), 59000, Lille, France.,Tumorigenesis and Resistance to Treatment Unit, Centre Oscar Lambret, 3 rue Frédéric Combemale, 59000, Lille, France
| | - François Anquez
- Laboratory of Physics of Lasers, Atoms and Molecules, UMR CNRS 8523, University of Lille, Villeneuve-d'Ascq, 59655, France
| | - Sylvain Julien
- University of Lille, U908-CPAC, Cell Plasticity and Cancer, F-59000, Lille, France.,Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France
| | - Amélie Bonnefond
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, 59000, Lille, France
| | - Mehdi Derhourhi
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, 59000, Lille, France
| | - Xuefen Le Bourhis
- University of Lille, U908-CPAC, Cell Plasticity and Cancer, F-59000, Lille, France.,Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France
| | - Chann Lagadec
- University of Lille, U908-CPAC, Cell Plasticity and Cancer, F-59000, Lille, France.,Institut National de la Santé et de la recherche Médicale (INSERM), U908, F-59000, Lille, France.,Institut pour la Recherche sur le Cancer de Lille (IRCL), 59000, Lille, France
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23
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Chiasson D, Giménez-Oya V, Bircheneder M, Bachmaier S, Studtrucker T, Ryan J, Sollweck K, Leonhardt H, Boshart M, Dietrich P, Parniske M. A unified multi-kingdom Golden Gate cloning platform. Sci Rep 2019; 9:10131. [PMID: 31300661 PMCID: PMC6626145 DOI: 10.1038/s41598-019-46171-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/19/2019] [Indexed: 12/21/2022] Open
Abstract
Assembling composite DNA modules from custom DNA parts has become routine due to recent technological breakthroughs such as Golden Gate modular cloning. Using Golden Gate, one can efficiently assemble custom transcription units and piece units together to generate higher-order assemblies. Although Golden Gate cloning systems have been developed to assemble DNA plasmids required for experimental work in model species, they are not typically applicable to organisms from other kingdoms. Consequently, a typical molecular biology laboratory working across kingdoms must use multiple cloning strategies to assemble DNA constructs for experimental assays. To simplify the DNA assembly process, we developed a multi-kingdom (MK) Golden Gate assembly platform for experimental work in species from the kingdoms Fungi, Eubacteria, Protista, Plantae, and Animalia. Plasmid backbone and part overhangs are consistent across the platform, saving both time and resources in the laboratory. We demonstrate the functionality of the system by performing a variety of experiments across kingdoms including genome editing, fluorescence microscopy, and protein interaction assays. The versatile MK system therefore streamlines the assembly of modular DNA constructs for biological assays across a range of model organisms.
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Affiliation(s)
- David Chiasson
- Faculty of Biology, Genetics, LMU Munich, D-82152, Martinsried, Germany. .,Department of Biology, Saint Mary's University, B3H 3C3, Halifax, Canada.
| | | | | | - Sabine Bachmaier
- Faculty of Biology, Genetics, LMU Munich, D-82152, Martinsried, Germany
| | - Tanja Studtrucker
- Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | - Joel Ryan
- Faculty of Biology and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, Großhaderner Str. 2, D-82152, Martinsried, Germany
| | | | - Heinrich Leonhardt
- Faculty of Biology and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, Großhaderner Str. 2, D-82152, Martinsried, Germany
| | - Michael Boshart
- Faculty of Biology, Genetics, LMU Munich, D-82152, Martinsried, Germany
| | - Petra Dietrich
- Department Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, D-91058, Erlangen, Germany
| | - Martin Parniske
- Faculty of Biology, Genetics, LMU Munich, D-82152, Martinsried, Germany.
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24
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Gilman J, Singleton C, Tennant RK, James P, Howard TP, Lux T, Parker DA, Love J. Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications. ACS Synth Biol 2019; 8:1175-1186. [PMID: 30995831 DOI: 10.1021/acssynbio.9b00061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Well-characterized promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterization to expand the promoter toolkit and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Here, we apply the method in Geobacillus thermoglucosidasius, a thermophilic organism with high potential as a synthetic biology chassis for industrial applications. Bioinformatic screening of G. kaustophilus, G. stearothermophilus, G. thermodenitrificans, and G. thermoglucosidasius resulted in the identification of 636 100 bp putative promoters, encompassing the genome-wide design space and lacking known transcription factor binding sites. Eighty of these sequences were characterized in vivo, and activities covered a 2-log range of predictable expression levels. Seven sequences were shown to function consistently regardless of the downstream coding sequence. Partition modeling identified sequence positions upstream of the canonical -35 and -10 consensus motifs that were predicted to strongly influence regulatory activity in Geobacillus, and artificial neural network and partial least squares regression models were derived to assess if there were a simple, forward, quantitative method for in silico prediction of promoter function. However, the models were insufficiently general to predict pre hoc promoter activity in vivo, most probably as a result of the relatively small size of the training data set compared to the size of the modeled design space.
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Affiliation(s)
- James Gilman
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Chloe Singleton
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Richard K. Tennant
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Paul James
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Thomas P. Howard
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle-upon-Tyne NE1 7RU, U.K
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich 85764, Germany
| | - David A. Parker
- Biodomain, Shell Technology Center Houston, 3333 Highway 6 South, Houston, Texas 77082-3101, United States
| | - John Love
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
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25
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Wagner N, Norlin N, Gierten J, de Medeiros G, Balázs B, Wittbrodt J, Hufnagel L, Prevedel R. Instantaneous isotropic volumetric imaging of fast biological processes. Nat Methods 2019; 16:497-500. [PMID: 31036959 DOI: 10.1038/s41592-019-0393-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/05/2019] [Indexed: 11/09/2022]
Abstract
To capture highly dynamic biological processes at cellular resolution is a recurring challenge in biology. Here we show that combining selective-volume illumination with simultaneous acquisition of orthogonal light fields yields three-dimensional images with high, isotropic spatial resolution and a significant reduction of reconstruction artefacts, thereby overcoming current limitations of light-field microscopy implementations. We demonstrate medaka heart and blood flow imaging at single-cell resolution and free of motion artefacts at volume rates of up to 200 Hz.
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Affiliation(s)
- Nils Wagner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nils Norlin
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Gustavo de Medeiros
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Bálint Balázs
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Lars Hufnagel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Robert Prevedel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Monterotondo, Italy.
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26
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Behrendorff JBYH, Sandoval-Ibañez OA, Sharma A, Pribil M. Membrane-Bound Protein Scaffolding in Diverse Hosts Using Thylakoid Protein CURT1A. ACS Synth Biol 2019; 8:611-620. [PMID: 30884945 DOI: 10.1021/acssynbio.8b00418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein scaffolding is a useful strategy for controlling the spatial arrangement of cellular components via protein-protein interactions. Protein scaffolding has primarily been used to colocalize soluble proteins in the cytoplasm, but many proteins require membrane association for proper function. Scaffolding at select membrane domains would provide an additional level of control over the distribution of proteins within a cell and could aid in exploiting numerous metabolic pathways that contain membrane-associated enzymes. We developed and characterized a membrane-bound protein scaffolding module based on the thylakoid protein CURT1A. This scaffolding module forms homo-oligomers in the membrane, causing proteins fused to CURT1A to cluster together at membrane surfaces. It is functional in diverse expression hosts and can scaffold proteins at thylakoid membranes in chloroplasts, endoplasmic reticulum in higher plants and Saccharomyces cerevisiae, and the inner membrane of Escherichia coli.
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Affiliation(s)
- James B. Y. H. Behrendorff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Omar A. Sandoval-Ibañez
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Anurag Sharma
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Mathias Pribil
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
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27
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Lischik CQ, Adelmann L, Wittbrodt J. Enhanced in vivo-imaging in medaka by optimized anaesthesia, fluorescent protein selection and removal of pigmentation. PLoS One 2019; 14:e0212956. [PMID: 30845151 PMCID: PMC6405165 DOI: 10.1371/journal.pone.0212956] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 02/12/2019] [Indexed: 02/07/2023] Open
Abstract
Fish are ideally suited for in vivo-imaging due to their transparency at early stages combined with a large genetic toolbox. Key challenges to further advance imaging are fluorophore selection, immobilization of the specimen and approaches to eliminate pigmentation. We addressed all three and identified the fluorophores and anaesthesia of choice by high throughput time-lapse imaging. Our results indicate that eGFP and mCherry are the best conservative choices for in vivo-fluorescence experiments, when availability of well-established antibodies and nanobodies matters. Still, mVenusNB and mGFPmut2 delivered highest absolute fluorescence intensities in vivo. Immobilization is of key importance during extended in vivo imaging. Here, traditional approaches are outperformed by mRNA injection of α-Bungarotoxin which allows a complete and reversible, transient immobilization. In combination with fully transparent juvenile and adult fish established by the targeted inactivation of both, oca2 and pnp4a via CRISPR/Cas9-mediated gene editing in medaka we could dramatically improve the state-of-the art imaging conditions in post-embryonic fish, now enabling light-sheet microscopy of the growing retina, brain, gills and inner organs in the absence of side effects caused by anaesthetic drugs or pigmentation.
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Affiliation(s)
- Colin Q Lischik
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany.,Heidelberg Biosciences International Graduate School, Heidelberg University, Heidelberg, Germany
| | - Leonie Adelmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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28
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Gutierrez-Triana JA, Tavhelidse T, Thumberger T, Thomas I, Wittbrodt B, Kellner T, Anlas K, Tsingos E, Wittbrodt J. Efficient single-copy HDR by 5' modified long dsDNA donors. eLife 2018; 7:39468. [PMID: 30156184 PMCID: PMC6125127 DOI: 10.7554/elife.39468] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/14/2018] [Indexed: 12/03/2022] Open
Abstract
CRISPR/Cas9 efficiently induces targeted mutations via non-homologous-end-joining but for genome editing, precise, homology-directed repair (HDR) of endogenous DNA stretches is a prerequisite. To favor HDR, many approaches interfere with the repair machinery or manipulate Cas9 itself. Using Medaka we show that the modification of 5’ ends of long dsDNA donors strongly enhances HDR, favors efficient single-copy integration by retaining a monomeric donor conformation thus facilitating successful gene replacement or tagging. CRISPR/Cas9 technology has revolutionized the ability of researchers to edit the DNA of any organism whose genome has already been sequenced. In the editing process, a section of RNA acts as a guide to match up to the location of the target DNA. The enzyme Cas9 then makes a cut in both strands of the DNA at this specific location. New segments of DNA can be introduced to the cell, incorporated into DNA ‘templates’. The cell uses the template to help it to heal the double-strand break, and in doing so adds the new DNA segment into the organism’s genome. A drawback of CRISPR/Cas9 is that it often introduces multiple copies of the new DNA segment into the genome because the templates can bind to each other before being pasted into place. In addition, some parts of the new DNA segment can be missed off during the editing process. However, most applications of CRISPR/Cas9 – for example, to replace a defective gene with a working version – require exactly one whole copy of the desired DNA to be inserted into the genome. In order to achieve more accurate CRISPR/Cas9 genome editing, Gutierrez-Triana, Tavhelidse, Thumberger et al. attached additional molecules to the end of the DNA template to shield the DNA from mistakes during editing. The modified template was used to couple a stem cell gene to a reporter that produces a green fluorescent protein into the genome of fish embryos. The fluorescent proteins made it easy to identify when the coupling was successful. Gutierrez-Triana et al. found that the additional molecules prevented multiple templates from joining together end to end, and ensured the full DNA segment was inserted into the genome. Furthermore, the results of the experiments showed that only one copy of the template was inserted into the DNA of the fish. In the future, the new template will allow DNA to be edited in a more controlled way both in basic research and in therapeutic applications.
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Affiliation(s)
| | | | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Isabelle Thomas
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Beate Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Tanja Kellner
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Kerim Anlas
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Erika Tsingos
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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29
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Luo Y, Qiu Y, Na R, Meerja F, Lu QS, Yang C, Tian L. A Golden Gate and Gateway double-compatible vector system for high throughput functional analysis of genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:117-126. [PMID: 29650149 DOI: 10.1016/j.plantsci.2018.03.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 06/08/2023]
Abstract
A major research topic nowadays is to study and understand the functions of the increasing number of predicted genes that have been discovered through the complete genome sequencing of many plant species. With the aim of developing tools for rapid and convenient gene function analysis, we have developed a set of "pGate" vectors based on the principle of Golden gate and Gateway cloning approaches. These vectors combine the positive aspects of both Golden gate and Gateway cloning strategies. pGate vectors can not only be used as Golden gate recipient vectors to assemble multiple DNA fragments in a pre-defined order, but they can also work as an entry vector to transfer the assembled DNA fragment(s) to a large number of already-existing, functionally diverse, Gateway compatible destination vectors without adding additional nucleotides during cloning. We show the pGate vectors are effective and convenient in several major aspects of gene function analyses, including BiFC (Bimolecular fluorescence complementation) to analyze protein-protein interaction, amiRNA (artificial microRNA) candidate screening and as assembly of CRISPR/Cas9 (Clustered regularly interspaced short palindromic repeats, CRISPR-associated protein-9 nuclease) system elements together for genome editing. The pGate system is a practical and flexible tool which can facilitate plant gene function research.
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Affiliation(s)
- Yanjie Luo
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada
| | - Yang Qiu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ren Na
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Farida Meerja
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada; Department of Biology, Western University, London, ON, N6A5B7, Canada
| | - Qing Shi Lu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada
| | - Chunyan Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, China
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, N5V4T3, Canada.
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30
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Gantner J, Ordon J, Ilse T, Kretschmer C, Gruetzner R, Löfke C, Dagdas Y, Bürstenbinder K, Marillonnet S, Stuttmann J. Peripheral infrastructure vectors and an extended set of plant parts for the Modular Cloning system. PLoS One 2018; 13:e0197185. [PMID: 29847550 PMCID: PMC5976141 DOI: 10.1371/journal.pone.0197185] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/27/2018] [Indexed: 11/21/2022] Open
Abstract
Standardized DNA assembly strategies facilitate the generation of multigene constructs from collections of building blocks in plant synthetic biology. A common syntax for hierarchical DNA assembly following the Golden Gate principle employing Type IIs restriction endonucleases was recently developed, and underlies the Modular Cloning and GoldenBraid systems. In these systems, transcriptional units and/or multigene constructs are assembled from libraries of standardized building blocks, also referred to as phytobricks, in several hierarchical levels and by iterative Golden Gate reactions. Here, a toolkit containing further modules for the novel DNA assembly standards was developed. Intended for use with Modular Cloning, most modules are also compatible with GoldenBraid. Firstly, a collection of approximately 80 additional phytobricks is provided, comprising e.g. modules for inducible expression systems, promoters or epitope tags. Furthermore, DNA modules were developed for connecting Modular Cloning and Gateway cloning, either for toggling between systems or for standardized Gateway destination vector assembly. Finally, first instances of a "peripheral infrastructure" around Modular Cloning are presented: While available toolkits are designed for the assembly of plant transformation constructs, vectors were created to also use coding sequence-containing phytobricks directly in yeast two hybrid interaction or bacterial infection assays. The presented material will further enhance versatility of hierarchical DNA assembly strategies.
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Affiliation(s)
- Johannes Gantner
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Jana Ordon
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Theresa Ilse
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Carola Kretschmer
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
| | - Ramona Gruetzner
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Christian Löfke
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Yasin Dagdas
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Katharina Bürstenbinder
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Sylvestre Marillonnet
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle (Saale), Germany
| | - Johannes Stuttmann
- Institute for Biology, Department of Plant Genetics, Martin Luther University Halle (Saale), Halle, Germany
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31
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Griffin JN, del Viso F, Duncan AR, Robson A, Hwang W, Kulkarni S, Liu KJ, Khokha MK. RAPGEF5 Regulates Nuclear Translocation of β-Catenin. Dev Cell 2018; 44:248-260.e4. [PMID: 29290587 PMCID: PMC5818985 DOI: 10.1016/j.devcel.2017.12.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 09/04/2017] [Accepted: 11/30/2017] [Indexed: 12/16/2022]
Abstract
Canonical Wnt signaling coordinates many critical aspects of embryonic development, while dysregulated Wnt signaling contributes to common diseases, including congenital malformations and cancer. The nuclear localization of β-catenin is the defining step in pathway activation. However, despite intensive investigation, the mechanisms regulating β-catenin nuclear transport remain undefined. In a patient with congenital heart disease and heterotaxy, a disorder of left-right patterning, we previously identified the guanine nucleotide exchange factor, RAPGEF5. Here, we demonstrate that RAPGEF5 regulates left-right patterning via Wnt signaling. In particular, RAPGEF5 regulates the nuclear translocation of β-catenin independently of both β-catenin cytoplasmic stabilization and the importin β1/Ran-mediated transport system. We propose a model whereby RAPGEF5 activates the nuclear GTPases, Rap1a/b, to facilitate the nuclear transport of β-catenin, defining a parallel nuclear transport pathway to Ran. Our results suggest new targets for modulating Wnt signaling in disease states.
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Affiliation(s)
- John N. Griffin
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA,Centre for Craniofacial and Regenerative Biology, King’s College London, London SE1 9RT, United Kingdom
| | - Florencia del Viso
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Anna R. Duncan
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Andrew Robson
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Woong Hwang
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Saurabh Kulkarni
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
| | - Karen J. Liu
- Centre for Craniofacial and Regenerative Biology, King’s College London, London SE1 9RT, United Kingdom
| | - Mustafa K. Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA,Correspondence to: Lead contact Mustafa Khokha,
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Kuri P, Schieber NL, Thumberger T, Wittbrodt J, Schwab Y, Leptin M. Dynamics of in vivo ASC speck formation. J Cell Biol 2017; 216:2891-2909. [PMID: 28701426 PMCID: PMC5584180 DOI: 10.1083/jcb.201703103] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 05/31/2017] [Accepted: 06/13/2017] [Indexed: 12/18/2022] Open
Abstract
The inflammasome adaptor ASC forms enormous intracellular complexes called specks. Live imaging of endogenous ASC in keratinocytes reveals speck formation dynamics and their lethal effects, as well as macrophages’ engulfment and digestion of the specks left behind by dead cells. Activated danger or pathogen sensors trigger assembly of the inflammasome adaptor ASC into specks, large signaling platforms considered hallmarks of inflammasome activation. Because a lack of in vivo tools has prevented the study of endogenous ASC dynamics, we generated a live ASC reporter through CRISPR/Cas9 tagging of the endogenous gene in zebrafish. We see strong ASC expression in the skin and other epithelia that act as barriers to insult. A toxic stimulus triggered speck formation and rapid pyroptosis in keratinocytes in vivo. Macrophages engulfed and digested that speck-containing, pyroptotic debris. A three-dimensional, ultrastructural reconstruction, based on correlative light and electron microscopy of the in vivo assembled specks revealed a compact network of highly intercrossed filaments, whereas pyrin domain (PYD) or caspase activation and recruitment domain alone formed filamentous aggregates. The effector caspase is recruited through PYD, whose overexpression induced pyroptosis but only after substantial delay. Therefore, formation of a single, compact speck and rapid cell-death induction in vivo requires a full-length ASC.
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Affiliation(s)
- Paola Kuri
- Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nicole L Schieber
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Electron Microscopy Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Maria Leptin
- Directors' Research Unit, European Molecular Biology Laboratory, Heidelberg, Germany .,Institute of Genetics, University of Cologne, Cologne, Germany.,European Molecular Biology Organization, Heidelberg, Germany
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Quaglia D, Ebert MCCJC, Mugford PF, Pelletier JN. Enzyme engineering: A synthetic biology approach for more effective library generation and automated high-throughput screening. PLoS One 2017; 12:e0171741. [PMID: 28178357 PMCID: PMC5298319 DOI: 10.1371/journal.pone.0171741] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 01/25/2017] [Indexed: 12/29/2022] Open
Abstract
The Golden Gate strategy entails the use of type IIS restriction enzymes, which cut outside of their recognition sequence. It enables unrestricted design of unique DNA fragments that can be readily and seamlessly recombined. Successfully employed in other synthetic biology applications, we demonstrate its advantageous use to engineer a biocatalyst. Hot-spots for mutations were individuated in three distinct regions of Candida antarctica lipase A (Cal-A), the biocatalyst chosen as a target to demonstrate the versatility of this recombination method. The three corresponding gene segments were subjected to the most appropriate method of mutagenesis (targeted or random). Their straightforward reassembly allowed combining products of different mutagenesis methods in a single round for rapid production of a series of diverse libraries, thus facilitating directed evolution. Screening to improve discrimination of short-chain versus long-chain fatty acid substrates was aided by development of a general, automated method for visual discrimination of the hydrolysis of varied substrates by whole cells.
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Affiliation(s)
- Daniela Quaglia
- Département de Chimie, Université de Montréal, Montréal, QC, Canada
- Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
| | - Maximilian C. C. J. C. Ebert
- Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC, Canada
| | - Paul F. Mugford
- DSM Nutritional Products, 101 Research Drive, Dartmouth, NS, Canada
| | - Joelle N. Pelletier
- Département de Chimie, Université de Montréal, Montréal, QC, Canada
- Center for Green Chemistry and Catalysis (CGCC), Université de Montréal, Montréal, QC, Canada
- PROTEO, The Québec Network for Research on Protein Function, Engineering and Applications, Québec, QC, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC, Canada
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34
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Inoue D, Stemmer M, Thumberger T, Ruppert T, Bärenz F, Wittbrodt J, Gruss OJ. Expression of the novel maternal centrosome assembly factor Wdr8 is required for vertebrate embryonic mitoses. Nat Commun 2017; 8:14090. [PMID: 28098238 PMCID: PMC5253655 DOI: 10.1038/ncomms14090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/29/2016] [Indexed: 02/07/2023] Open
Abstract
The assembly of the first centrosome occurs upon fertilisation when male centrioles recruit pericentriolar material (PCM) from the egg cytoplasm. The mechanisms underlying the proper assembly of centrosomes during early embryogenesis remain obscure. We identify Wdr8 as a novel maternally essential protein that is required for centrosome assembly during embryonic mitoses of medaka (Oryzias latipes). By CRISPR-Cas9-mediated knockout, maternal/zygotic Wdr8-null (m/zWdr8-/-) blastomeres exhibit severe defects in centrosome structure that lead to asymmetric division, multipolar mitotic spindles and chromosome alignment errors. Via its WD40 domains, Wdr8 interacts with the centriolar satellite protein SSX2IP. Combining targeted gene knockout and in vivo reconstitution of the maternally essential Wdr8-SSX2IP complex reveals an essential link between maternal centrosome proteins and the stability of the zygotic genome for accurate vertebrate embryogenesis. Our approach provides a way of distinguishing maternal from paternal effects in early embryos and should contribute to understanding molecular defects in human infertility.
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Affiliation(s)
- Daigo Inoue
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Manuel Stemmer
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Thomas Ruppert
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Felix Bärenz
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg 69120, Germany
| | - Oliver J Gruss
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg D-69120, Germany.,Institute of Genetics, University of Bonn, Karlrobert-Kreiten-Straße 13, Bonn 53115, Germany
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35
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Wang HY, Li Y, Xue T, Cheng N, Du HN. Construction of a series of pCS2+ backbone-based Gateway vectors for overexpressing various tagged proteins in vertebrates. Acta Biochim Biophys Sin (Shanghai) 2016; 48:1128-1134. [PMID: 27797719 DOI: 10.1093/abbs/gmw107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/25/2016] [Accepted: 09/08/2016] [Indexed: 11/13/2022] Open
Abstract
Gateway vectors have been extensively developed to facilitate gene cloning in numerous species; however, a universal system that is compatible for multiple organisms was lacking. As a multipurpose expression vector, pCS2+ backbone-based expression plasmids are widely used for high-level expression of messenger RNAs (mRNAs) or proteins in mammalian/avian culture cells or Xenopus/zebrafish embryos. To date, a suite of vectors with pCS2+ backbone applicable for Gateway cloning system were unavailable yet. Here, we generated a set of Gateway destination vectors, named as pGCS (plasmids of Gateway in pCS2+) vectors, which can be fused to a choice of frequently used amino- or carboxyl-terminal tags, including MYC, HA, FLAG, His, GST, as well as eGFP fluorescent epitope. The systematic generation of this set of pCS2+ backbone-based Gateway destination vectors allows for in vitro recombination of DNA with high speed, accuracy, and reliability compared with the traditional 'digestion-ligation' cloning approach. Thus, our system accelerates the production of functional proteins, which could be widely expressed in a large variety of vertebrate organisms without tediously transferring genes into different expression vectors. Moreover, we make this series of Gateway vectors available to the research community via the non-profit Addgene Plasmid Repository.
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Affiliation(s)
- Hong-Yan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yang Li
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Tingling Xue
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ningyan Cheng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
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36
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Garanina EE, Mukhamedshina YO, Salafutdinov II, Kiyasov AP, Lima LM, Reis HJ, Palotás A, Islamov RR, Rizvanov AA. Construction of recombinant adenovirus containing picorna-viral 2A-peptide sequence for the co-expression of neuro-protective growth factors in human umbilical cord blood cells. Spinal Cord 2015; 54:423-30. [PMID: 26439843 DOI: 10.1038/sc.2015.162] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/18/2015] [Accepted: 07/31/2015] [Indexed: 11/09/2022]
Abstract
STUDY DESIGN Experimental study. OBJECTIVE Several neuro-degenerative disorders such as Alzheimer's dementia, Parkinson's disease and amyotrophic lateral sclerosis (ALS) are associated with genetic mutations, and replacing or disrupting defective sequences might offer therapeutic benefits. Single gene delivery has so far failed to achieve significant clinical improvements in humans, leading to the advent of co-expression of multiple therapeutic genes. Co-transfection using two or more individual constructs might inadvertently result in disproportionate delivery of the products into the cells. To prevent this, and in order to rule out interference among the many promoters with varying strength, expressing multiple proteins in equimolar amounts can be achieved by linking open reading frames under the control of only one promoter. SETTING Kazan, Russian Federation. METHODS Here we describe a strategy for adeno-viral co-expression of vascular endothelial growth factor (VEGF) and fibroblast growth factor 2 (FGF2) interconnected through picorna-viral 2A-amino-acid sequence in transfected human umbilical cord blood mono-nuclear cells (hUCB-MCs). RESULTS Presence of both growth factors, as well as absence of immune response to 2A-antigen, was demonstrated after 28-52 days. Following injection of hUCB-MCs into ALS transgenic mice, co-expression of VEGF and FGF2, as well as viable xeno-transplanted cells, were observed in the spinal cord after 1 month. CONCLUSION These results suggest that recombinant adeno-virus containing 2A-sequences could serve as a promising alternative in regenerative medicine for the delivery of therapeutic molecules to treat neurodegenerative diseases, such as ALS.
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Affiliation(s)
- E E Garanina
- Kazan Federal University, Kazan, Russian Federation
| | | | | | - A P Kiyasov
- Kazan Federal University, Kazan, Russian Federation
| | - L M Lima
- Universidade Federal de Viçosa, Viçosa, Brazil
| | - H J Reis
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - A Palotás
- Kazan Federal University, Kazan, Russian Federation.,Asklepios-Med (Private Medical Practice and Research Center), Szeged, Hungary
| | - R R Islamov
- Kazan State Medical University, Kazan, Russian Federation
| | - A A Rizvanov
- Kazan Federal University, Kazan, Russian Federation
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37
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Caroti F, Urbansky S, Wosch M, Lemke S. Germ line transformation and in vivo labeling of nuclei in Diptera: report on Megaselia abdita (Phoridae) and Chironomus riparius (Chironomidae). Dev Genes Evol 2015; 225:179-86. [PMID: 26044750 PMCID: PMC4460289 DOI: 10.1007/s00427-015-0504-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/20/2015] [Indexed: 11/28/2022]
Abstract
To understand how and when developmental traits of the fruit fly Drosophila melanogaster originated during the course of insect evolution, similar traits are functionally studied in variably related satellite species. The experimental toolkit available for relevant fly models typically comprises gene expression and loss as well as gain-of-function analyses. Here, we extend the set of available molecular tools to piggyBac-based germ line transformation in two satellite fly models, Megaselia abdita and Chironomus riparius. As proof-of-concept application, we used a Gateway variant of the piggyBac transposon vector pBac{3xP3-eGFPafm} to generate a transgenic line that expresses His2Av-mCherry as fluorescent nuclear reporter ubiquitously in the gastrulating embryo of M. abdita. Our results open two phylogenetically important nodes of the insect order Diptera for advanced developmental evolutionary genetics.
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Affiliation(s)
- Francesca Caroti
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Silvia Urbansky
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Maike Wosch
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Steffen Lemke
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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38
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Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL. CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool. PLoS One 2015; 10:e0124633. [PMID: 25909470 PMCID: PMC4409221 DOI: 10.1371/journal.pone.0124633] [Citation(s) in RCA: 630] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 03/17/2015] [Indexed: 12/26/2022] Open
Abstract
Engineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5’ end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a sequence of twenty nucleotides can occur multiple times in a given genome and some mismatches seem to be accepted by the CRISPR/Cas9 complex, an efficient and reliable in silico selection and evaluation of the targeting site is key prerequisite for the experimental success. Here we present the CRISPR/Cas9 target online predictor (CCTop, http://crispr.cos.uni-heidelberg.de) to overcome limitations of already available tools. CCTop provides an intuitive user interface with reasonable default parameters that can easily be tuned by the user. From a given query sequence, CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. Thus, CCTop provides the bench biologist with a tool for the rapid and efficient identification of high quality target sites.
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Affiliation(s)
- Manuel Stemmer
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Maria Del Sol Keyer
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Juan L Mateo
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
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39
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Reinhardt R, Centanin L, Tavhelidse T, Inoue D, Wittbrodt B, Concordet JP, Martinez-Morales JR, Wittbrodt J. Sox2, Tlx, Gli3, and Her9 converge on Rx2 to define retinal stem cells in vivo. EMBO J 2015; 34:1572-88. [PMID: 25908840 PMCID: PMC4474531 DOI: 10.15252/embj.201490706] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 04/01/2015] [Indexed: 12/21/2022] Open
Abstract
Transcriptional networks defining stemness in adult neural stem cells (NSCs) are largely unknown. We used the proximal cis-regulatory element (pCRE) of the retina-specific homeobox gene 2 (rx2) to address such a network. Lineage analysis in the fish retina identified rx2 as marker for multipotent NSCs. rx2-positive cells located in the peripheral ciliary marginal zone behave as stem cells for the neuroretina, or the retinal pigmented epithelium. We identified upstream regulators of rx2 interrogating the rx2 pCRE in a trans-regulation screen and focused on four TFs (Sox2, Tlx, Gli3, and Her9) activating or repressing rx2 expression. We demonstrated direct interaction of the rx2 pCRE with the four factors in vitro and in vivo. By conditional mosaic gain- and loss-of-function analyses, we validated the activity of those factors on regulating rx2 transcription and consequently modulating neuroretinal and RPE stem cell features. This becomes obvious by the rx2-mutant phenotypes that together with the data presented above identify rx2 as a transcriptional hub balancing stemness of neuroretinal and RPE stem cells in the adult fish retina.
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Affiliation(s)
- Robert Reinhardt
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Lázaro Centanin
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Daigo Inoue
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Beate Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
| | | | | | - Joachim Wittbrodt
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Heidelberg, Germany
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40
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Bringing functions together with fusion enzymes—from nature’s inventions to biotechnological applications. Appl Microbiol Biotechnol 2014; 99:1545-56. [DOI: 10.1007/s00253-014-6315-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/04/2014] [Accepted: 12/09/2014] [Indexed: 12/18/2022]
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41
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Quin MB, Schmidt-Dannert C. Designer microbes for biosynthesis. Curr Opin Biotechnol 2014; 29:55-61. [PMID: 24646570 DOI: 10.1016/j.copbio.2014.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/19/2014] [Accepted: 02/20/2014] [Indexed: 01/01/2023]
Abstract
Microbes have long been adapted for the biosynthetic production of useful compounds. There is increasing demand for the rapid and cheap microbial production of diverse molecules in an industrial setting. Microbes can now be designed and engineered for a particular biosynthetic purpose, thanks to recent developments in genome sequencing, metabolic engineering, and synthetic biology. Advanced tools exist for the genetic manipulation of microbes to create novel metabolic circuits, making new products accessible. Metabolic processes can be optimized to increase yield and balance pathway flux. Progress is being made towards the design and creation of fully synthetic microbes for biosynthetic purposes. Together, these emerging technologies will facilitate the production of designer microbes for biosynthesis.
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Affiliation(s)
- Maureen B Quin
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA.
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