1
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Rozich E, Randolph LK, Insolera R. An optimized temporally controlled Gal4 system in Drosophila reveals degeneration caused by adult-onset neuronal Vps13D knockdown. Front Neurosci 2023; 17:1204068. [PMID: 37457002 PMCID: PMC10339317 DOI: 10.3389/fnins.2023.1204068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Mutations in the human gene VPS13D cause the adult-onset neurodegenerative disease ataxia. Our previous work showed that disruptions in the Vps13D gene in Drosophila neurons causes mitochondrial defects. However, developmental lethality caused by Vps13D loss limited our understanding of the long-term physiological effects of Vps13D perturbation in neurons. Here, we optimized a previously generated system to temporally knock down Vps13D expression precisely in adult Drosophila neurons using a modification to the Gal4/UAS system. Adult-onset activation of Gal4 was enacted using the chemically-inducible tool which fuses a destabilization-domain to the Gal4 repressor Gal80 (Gal80-DD). Optimization of the Gal80-DD tool shows that feeding animals the DD-stabilizing drug trimethoprim (TMP) during development and rearing at a reduced temperature maximally represses Gal4 activity. Temperature shift and removal of TMP from the food after eclosion robustly activates Gal4 expression in adult neurons. Using the optimized Gal80-DD system, we find that adult-onset Vps13D RNAi expression in neurons causes the accumulation of mitophagy intermediates, progressive deficits in locomotor activity, early lethality, and brain vacuolization characteristic of neurodegeneration. The development of this optimized system allows us to more precisely examine the degenerative phenotypes caused by Vps13D disruption, and can likely be utilized in the future for other genes associated with neurological diseases whose manipulation causes developmental lethality in Drosophila.
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Affiliation(s)
- Emily Rozich
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
| | - Lynsey K. Randolph
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Ryan Insolera
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI, United States
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2
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Huang Z, Wang W, Xu P, Gong S, Hu Y, Liu Y, Su F, Anjum KM, Deng WM, Yang S, Liu J, Jiao R, Chen J. Drosophila Ectoderm-expressed 4 modulates JAK/STAT pathway and protects flies against Drosophila C virus infection. Front Immunol 2023; 14:1135625. [PMID: 36817462 PMCID: PMC9937023 DOI: 10.3389/fimmu.2023.1135625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Sterile alpha and HEAT/Armadillo motif-containing protein (SARM) is conserved in evolution and negatively regulates TRIF-dependent Toll signaling in mammals. The SARM protein from Litopenaeus vannamei and its Drosophila orthologue Ectoderm-expressed (Ect4) are also involved in immune defense against pathogen infection. However, the functional mechanism of the protective effect remains unclear. In this study, we show that Ect4 is essential for the viral load in flies after a Drosophila C virus (DCV) infection. Viral load is increased in Ect4 mutants resulting in higher mortality rates than wild-type. Overexpression of Ect4 leads to a suppression of virus replication and thus improves the survival rate of the animals. Ect4 is required for the viral induction of STAT-responsive genes, TotA and TotM. Furthermore, Ect4 interacts with Stat92E, affecting the tyrosine phosphorylation and nuclear translocation of Stat92E in S2 cells. Altogether, our study identifies the adaptor protein Ect4 of the Toll pathway contributes to resistance to viral infection and regulates JAK/STAT signaling pathway.
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Affiliation(s)
- Zongliang Huang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China,Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Wei Wang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China,Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, Fujian, China
| | - Pengpeng Xu
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Shangyu Gong
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yingshan Hu
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yan Liu
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fang Su
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Khalid Mahmood Anjum
- Department of Wildlife and Ecology, University of Veterinary and Animal Sciences, Lahore, Punjab, Pakistan
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Suping Yang
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, Fujian, China
| | - Jiyong Liu
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China,*Correspondence: Jiyong Liu, ; Renjie Jiao, ; Jianming Chen,
| | - Renjie Jiao
- Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China,*Correspondence: Jiyong Liu, ; Renjie Jiao, ; Jianming Chen,
| | - Jianming Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, Fujian, China,Sino-French Hoffmann Institute, School of Basic Sciences, Guangzhou Medical University, Guangzhou, Guangdong, China,*Correspondence: Jiyong Liu, ; Renjie Jiao, ; Jianming Chen,
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3
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Lin J, Yao Z, Lyu X, Ye L, Yu H. Development of a dual temperature control system for isoprene biosynthesis in Saccharomyces cerevisiae. Front Chem Sci Eng 2021. [DOI: 10.1007/s11705-021-2088-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Driesschaert B, Mergan L, Temmerman L. Conditional gene expression in invertebrate animal models. J Genet Genomics 2021; 48:14-31. [PMID: 33814307 DOI: 10.1016/j.jgg.2021.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/11/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
A mechanistic understanding of biology requires appreciating spatiotemporal aspects of gene expression and its functional implications. Conditional expression allows for (ir)reversible switching of genes on or off, with the potential of spatial and/or temporal control. This provides a valuable complement to the more often used constitutive gene (in)activation through mutagenesis, providing tools to answer a wider array of research questions across biological disciplines. Spatial and/or temporal control are granted primarily by (combinations of) specific promoters, temperature regimens, compound addition, or illumination. The use of such genetic tool kits is particularly widespread in invertebrate animal models because they can be applied to study biological processes in short time frames and on large scales, using organisms amenable to easy genetic manipulation. Recent years witnessed an exciting expansion and optimization of such tools, of which we provide a comprehensive overview and discussion regarding their use in invertebrates. The mechanism, applicability, benefits, and drawbacks of each of the systems, as well as further developments to be expected in the foreseeable future, are highlighted.
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Affiliation(s)
- Brecht Driesschaert
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59 - Box 2465, B-3000 Leuven, Belgium
| | - Lucas Mergan
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59 - Box 2465, B-3000 Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, University of Leuven (KU Leuven), Naamsestraat 59 - Box 2465, B-3000 Leuven, Belgium.
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5
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Zhang XB, Dong W, Li KX, Wang JJ, Shen J, Moussian B, Zhang JZ. Flexible manipulation of Omb levels in the endogenous expression region of Drosophila wing by combinational overexpression and suppression strategy. INSECT SCIENCE 2020; 27:14-21. [PMID: 31246335 DOI: 10.1111/1744-7917.12705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 06/09/2023]
Abstract
Manipulating an exogenous or endogenous gene of interest at a defined level is critical for a wide variety of experiments. The Gal4/UAS system has been widely used to direct gene expression for studying complex genetic and biological problems in Drosophila melanogaster and other model organisms. Driven by a given tissue-specific Gal4, expressing UAS-transgene or UAS-RNAi (RNA interference) could be used to up- or down-regulate target gene expression, respectively. However, the efficiency of the Gal4/UAS system is roughly predefined by properties of transposon vector constructs and the insertion site in the transgenic stock. Here, we describe a simple way to modulate optomotor blind (omb) expression levels in its endogenous expression region of the wing disc. We co-expressed UAS-omb and UAS-omb-RNAi together under the control of dpp-Gal4 driver which is expressed in the omb expression region of the wing pouch. The repression effect is more sensitive to temperature than that of overexpression. At low temperature, overexpression plays a dominant role but the efficiency is attenuated by UAS-omb-RNAi. In contrast, at high temperature RNAi predominates in gene expression regulation. By this strategy, we could manipulate omb expression levels at a moderate level. It allows us to manipulate omb expression levels in the same tissue between overexpression and repression at different stages by temperature control.
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Affiliation(s)
- Xu-Bo Zhang
- Institute of Applied Biology, College of Life Science, Shanxi University, Taiyuan, China
| | - Wei Dong
- Institute of Applied Biology, College of Life Science, Shanxi University, Taiyuan, China
- Applied Zoology, Technical University Dresden, Zellescher Weg 20b, Dresden, Germany
- iBV, University of Nice Sophia-Antipolis, Parc Valrose, Nice, France
| | - Kai-Xia Li
- Institute of Applied Biology, College of Life Science, Shanxi University, Taiyuan, China
| | - Juan-Juan Wang
- Institute of Applied Biology, College of Life Science, Shanxi University, Taiyuan, China
| | - Jie Shen
- Institute of Applied Biology, College of Life Science, Shanxi University, Taiyuan, China
- Department of Entomology, China Agricultural University, Beijing, China
| | - Bernard Moussian
- Institute of Applied Biology, College of Life Science, Shanxi University, Taiyuan, China
- Applied Zoology, Technical University Dresden, Zellescher Weg 20b, Dresden, Germany
- iBV, University of Nice Sophia-Antipolis, Parc Valrose, Nice, France
| | - Jian-Zhen Zhang
- Institute of Applied Biology, College of Life Science, Shanxi University, Taiyuan, China
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6
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Jones MH, O'Toole ET, Fabritius AS, Muller EG, Meehl JB, Jaspersen SL, Winey M. Key phosphorylation events in Spc29 and Spc42 guide multiple steps of yeast centrosome duplication. Mol Biol Cell 2018; 29:2280-2291. [PMID: 30044722 PMCID: PMC6249810 DOI: 10.1091/mbc.e18-05-0296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Phosphorylation modulates many cellular processes during cell cycle progression. The yeast centrosome (called the spindle pole body, SPB) is regulated by the protein kinases Mps1 and Cdc28/Cdk1 as it nucleates microtubules to separate chromosomes during mitosis. Previously we completed an SPB phosphoproteome, identifying 297 sites on 17 of the 18 SPB components. Here we describe mutagenic analysis of phosphorylation events on Spc29 and Spc42, two SPB core components that were shown in the phosphoproteome to be heavily phosphorylated. Mutagenesis at multiple sites in Spc29 and Spc42 suggests that much of the phosphorylation on these two proteins is not essential but enhances several steps of mitosis. Of the 65 sites examined on both proteins, phosphorylation of the Mps1 sites Spc29-T18 and Spc29-T240 was shown to be critical for function. Interestingly, these two sites primarily influence distinct successive steps; Spc29-T240 is important for the interaction of Spc29 with Spc42, likely during satellite formation, and Spc29-T18 facilitates insertion of the new SPB into the nuclear envelope and promotes anaphase spindle elongation. Phosphorylation sites within Cdk1 motifs affect function to varying degrees, but mutations only have significant effects in the presence of an MPS1 mutation, supporting a theme of coregulation by these two kinases.
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Affiliation(s)
- Michele Haltiner Jones
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Eileen T O'Toole
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Amy S Fabritius
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616
| | - Eric G Muller
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | - Janet B Meehl
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
| | - Sue L Jaspersen
- Stowers Institute for Medical Research, Kansas City, MO 64110.,Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Mark Winey
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309
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7
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Zhou P, Xie W, Yao Z, Zhu Y, Ye L, Yu H. Development of a temperature-responsive yeast cell factory using engineered Gal4 as a protein switch. Biotechnol Bioeng 2018; 115:1321-1330. [PMID: 29315481 DOI: 10.1002/bit.26544] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/08/2017] [Accepted: 01/02/2018] [Indexed: 01/11/2023]
Abstract
Conflict between cell growth and product accumulation is frequently encountered in biosynthesis of secondary metabolites. Herein, a temperature-dependent dynamic control strategy was developed by modifying the GAL regulation system to facilitate two-stage fermentation in yeast. A temperature-sensitive Gal4 mutant Gal4M9 was created by directed evolution, and used as a protein switch in ΔGAL80 yeast. After EGFP-reported validation of its temperature-responsive induction capability, the sensitivity and stringency of this system in multi-gene pathway regulation was tested, using lycopene as an example product. When Gal4M9 was used to control the expression of PGAL -driven pathway genes, growth and production was successfully decoupled upon temperature shift during fermentation, accumulating 44% higher biomass and 177% more lycopene than the control strain with wild-type Gal4. This is the first example of adopting temperature as an input signal for metabolic pathway regulation in yeast cell factories.
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Affiliation(s)
- Pingping Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, P.R. China
| | - Wenping Xie
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, P.R. China
| | - Zhen Yao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, P.R. China
| | - Yongqiang Zhu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, P.R. China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, P.R. China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, P.R. China
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8
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Wong J, Chen X, Truong K. Engineering a temperature sensitive tobacco etch virus protease. Protein Eng Des Sel 2017; 30:705-712. [PMID: 29040785 DOI: 10.1093/protein/gzx050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/26/2017] [Indexed: 11/12/2022] Open
Abstract
Since tobacco etch virus protease (TEVp) has a high specificity and efficiency in cleaving its target substrates, many groups have attempted to engineer conditional control of its activity. Temperature induction is widely used for modulating gene function because it has fast temporal response, good penetrability and applicability to many model organisms. Here, we engineered a temperature sensitive TEVp (tsTEVp) by using N-terminal truncations to TEVp that achieved efficient proteolysis on a timescale of 4 h after 30°C induction, while remaining relatively inactive at 37°C. As demonstration, tsTEVp was used to generate temperature-induced biological responses for protein translocation, protein degradation and Ca2+-mediated cellular blebbing. Lastly, tsTEVp and their engineered target substrates could find applications in engineered synthetic biological systems.
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Affiliation(s)
- J Wong
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - X Chen
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9
| | - K Truong
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, Canada M5S 3G9.,Edward S. Rogers, Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Circle, Toronto, Ontario, Canada M5S 3G4
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9
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Abstract
Cold-sensitive phenotypes have helped us understand macromolecular assembly and biological phenomena, yet few attempts have been made to understand the basis of cold sensitivity or to elicit it by design. We report a method for rational design of cold-sensitive phenotypes. The method involves generation of partial loss-of-function mutants, at either buried or functional sites, coupled with selective overexpression strategies. The only essential input is amino acid sequence, although available structural information can be used as well. The method has been used to elicit cold-sensitive mutants of a variety of proteins, both monomeric and dimeric, and in multiple organisms, namely Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster This simple, yet effective technique of inducing cold sensitivity eliminates the need for complex mutations and provides a plausible molecular mechanism for eliciting cold-sensitive phenotypes.
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10
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Abstract
Since its introduction in 1993, the GAL4 system has become an essential part of the Drosophila geneticist's toolkit. Widely used to drive gene expression in a multitude of cell- and tissue-specific patterns, the system has been adapted and extended to form the basis of many modern tools for the manipulation of gene expression in Drosophila and other model organisms.
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11
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Legaz S, Exposito JY, Borel A, Candusso MP, Megy S, Montserret R, Lahaye V, Terzian C, Verrier B. A purified truncated form of yeast Gal4 expressed in Escherichia coli and used to functionalize poly(lactic acid) nanoparticle surface is transcriptionally active in cellulo. Protein Expr Purif 2015; 113:94-101. [PMID: 26002116 DOI: 10.1016/j.pep.2015.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/06/2015] [Accepted: 05/12/2015] [Indexed: 11/24/2022]
Abstract
Gal4/UAS system is a powerful tool for the analysis of numerous biological processes. Gal4 is a large yeast transcription factor that activates genes including UAS sequences in their promoter. Here, we have synthesized a minimal form of Gal4 DNA sequence coding for the binding and dimerization regions, but also part of the transcriptional activation domain. This truncated Gal4 protein was expressed as inclusion bodies in Escherichia coli. A structured and active form of this recombinant protein was purified and used to cover poly(lactic acid) (PLA) nanoparticles. In cellulo, these Gal4-vehicles were able to activate the expression of a Green Fluorescent Protein (GFP) gene under the control of UAS sequences, demonstrating that the decorated Gal4 variant can be delivery into cells where it still retains its transcription factor capacities. Thus, we have produced in E. coli and purified a short active form of Gal4 that retains its functions at the surface of PLA-nanoparticles in cellular assay. These decorated Gal4-nanoparticles will be useful to decipher their tissue distribution and their potential after ingestion or injection in UAS-GFP recombinant animal models.
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Affiliation(s)
- Sophie Legaz
- Institut de Biologie et Chimie des Protéines, FR3302, SFR BioSciences (UMS3444/US8) Gerland-Lyon Sud, Université de Lyon 1, Lyon, France; Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, CNRS UMR 5305, 7 passage du Vercors, 69367 Lyon, France
| | - Jean-Yves Exposito
- Institut de Biologie et Chimie des Protéines, FR3302, SFR BioSciences (UMS3444/US8) Gerland-Lyon Sud, Université de Lyon 1, Lyon, France; Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, CNRS UMR 5305, 7 passage du Vercors, 69367 Lyon, France
| | - Agnès Borel
- Institut de Biologie et Chimie des Protéines, FR3302, SFR BioSciences (UMS3444/US8) Gerland-Lyon Sud, Université de Lyon 1, Lyon, France; Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, CNRS UMR 5305, 7 passage du Vercors, 69367 Lyon, France
| | - Marie-Pierre Candusso
- Institut de Biologie et Chimie des Protéines, FR3302, SFR BioSciences (UMS3444/US8) Gerland-Lyon Sud, Université de Lyon 1, Lyon, France; Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086, 7 passage du Vercors, 69367 Lyon, France
| | - Simon Megy
- Institut de Biologie et Chimie des Protéines, FR3302, SFR BioSciences (UMS3444/US8) Gerland-Lyon Sud, Université de Lyon 1, Lyon, France; Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, CNRS UMR 5305, 7 passage du Vercors, 69367 Lyon, France
| | - Roland Montserret
- Institut de Biologie et Chimie des Protéines, FR3302, SFR BioSciences (UMS3444/US8) Gerland-Lyon Sud, Université de Lyon 1, Lyon, France; Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086, 7 passage du Vercors, 69367 Lyon, France
| | - Vincent Lahaye
- Institut de Biologie et Chimie des Protéines, FR3302, SFR BioSciences (UMS3444/US8) Gerland-Lyon Sud, Université de Lyon 1, Lyon, France; Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, CNRS UMR 5305, 7 passage du Vercors, 69367 Lyon, France
| | - Christophe Terzian
- Institut de Biologie et Chimie des Protéines, FR3302, SFR BioSciences (UMS3444/US8) Gerland-Lyon Sud, Université de Lyon 1, Lyon, France; Infection et Evolution des Génomes Viraux, INRA-UCBL UMR754, 69367 Lyon, France
| | - Bernard Verrier
- Institut de Biologie et Chimie des Protéines, FR3302, SFR BioSciences (UMS3444/US8) Gerland-Lyon Sud, Université de Lyon 1, Lyon, France; Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique, CNRS UMR 5305, 7 passage du Vercors, 69367 Lyon, France.
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12
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Improved and expanded Q-system reagents for genetic manipulations. Nat Methods 2015; 12:219-22, 5 p following 222. [PMID: 25581800 PMCID: PMC4344399 DOI: 10.1038/nmeth.3250] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 12/01/2014] [Indexed: 12/25/2022]
Abstract
The Q system is a repressible binary expression system for transgenic manipulations in living organisms. Through protein engineering and in vivo functional tests, we report here variants of the Q-system transcriptional activator, including QF2, for driving strong and ubiquitous expression in all Drosophila tissues. Our QF2, Gal4QF and LexAQF chimeric transcriptional activators substantially enrich the toolkit available for transgenic regulation in Drosophila melanogaster.
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13
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Tan KP, Khare S, Varadarajan R, Madhusudhan MS. TSpred: a web server for the rational design of temperature-sensitive mutants. Nucleic Acids Res 2014; 42:W277-84. [PMID: 24782523 PMCID: PMC4086094 DOI: 10.1093/nar/gku319] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Temperature sensitive (Ts) mutants of proteins provide experimentalists with a powerful and reversible way of conditionally expressing genes. The technique has been widely used in determining the role of gene and gene products in several cellular processes. Traditionally, Ts mutants are generated by random mutagenesis and then selected though laborious large-scale screening. Our web server, TSpred (http://mspc.bii.a-star.edu.sg/TSpred/), now enables users to rationally design Ts mutants for their proteins of interest. TSpred uses hydrophobicity and hydrophobic moment, deduced from primary sequence and residue depth, inferred from 3D structures to predict/identify buried hydrophobic residues. Mutating these residues leads to the creation of Ts mutants. Our method has been experimentally validated in 36 positions in six different proteins. It is an attractive proposition for Ts mutant engineering as it proposes a small number of mutations and with high precision. The accompanying web server is simple and intuitive to use and can handle proteins and protein complexes of different sizes.
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Affiliation(s)
- Kuan Pern Tan
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671 School of Computer Engineering, Nanyang Technological University, Singapore 639798
| | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Mallur Srivatsan Madhusudhan
- Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, Singapore 138671 Indian Institute of Science Education and Research, Pune 411008, India Department of Biological Sciences, National University of Singapore, Singapore 117543
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14
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Residue specific contributions to stability and activity inferred from saturation mutagenesis and deep sequencing. Curr Opin Struct Biol 2014; 24:63-71. [DOI: 10.1016/j.sbi.2013.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 11/25/2013] [Accepted: 12/03/2013] [Indexed: 12/23/2022]
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15
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Abstract
Necrotic cell death (necrosis) occurs in many acute-onset diseases. However, our poor understanding of its mechanism has greatly limited medical interventions. Here we describe two methods to establish necrosis models in Drosophila. Our strategy is to overload calcium by expression of leaky cation channels.
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Affiliation(s)
- Kai Liu
- State Key Lab of Biomembrane and Membrane Biotechnology, School of Life Sciences, Peking University, Beijing, China
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16
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Hallacli E, Lipp M, Georgiev P, Spielman C, Cusack S, Akhtar A, Kadlec J. Msl1-Mediated Dimerization of the Dosage Compensation Complex Is Essential for Male X-Chromosome Regulation in Drosophila. Mol Cell 2012; 48:587-600. [DOI: 10.1016/j.molcel.2012.09.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 07/09/2012] [Accepted: 09/10/2012] [Indexed: 10/27/2022]
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17
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Le Bras S, Rondanino C, Kriegel-Taki G, Dussert A, Le Borgne R. Genetic identification of intracellular trafficking regulators involved in notch dependent binary cell fate acquisition following asymmetric cell division. J Cell Sci 2012; 125:4886-901. [DOI: 10.1242/jcs.110171] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Notch signaling is involved in numerous cellular processes during development and throughout adult life. Although ligands and receptors are largely expressed in the whole organism, activation of Notch receptors only takes place in a subset of cells and/or tissues and is accurately regulated in time and space. Previous studies have demonstrated that endocytosis and recycling of both ligands and/or receptors are essential for this regulation. However, the precise endocytic routes, compartments and regulators involved in the spatio temporal regulation are largely unknown.
In order to identify Notch signaling intracellular trafficking regulators, we have undertaken a tissue-specific dsRNA genetic screen against candidates potentially involved in endocytosis and recycling within the endolysosomal pathway. dsRNA against 418 genes was induced in Drosophila melanogaster sensory organ lineage in which Notch signaling regulates binary cell fate acquisition. Gain- or loss-of Notch signaling phenotypes were observed in adult sensory organs for 113 of them. Furthermore, 26 genes presented a change in the steady state localization of Notch, Sanpodo, a Notch co-factor, and/or Delta in the pupal lineage. In particular, we identified 20 genes with previously unknown function in Drosophila melanogaster intracellular trafficking. Among them, we identified CG2747 and show that it regulates the localization of clathrin adaptor AP-1 complex, a negative regulator of Notch signaling. All together, our results further demonstrate the essential function of intracellular trafficking in regulating Notch signaling-dependent binary cell fate acquisition and constitute an additional step toward the elucidation of the routes followed by Notch receptor and ligands to signal.
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Venken KJ, Simpson JH, Bellen HJ. Genetic manipulation of genes and cells in the nervous system of the fruit fly. Neuron 2011; 72:202-30. [PMID: 22017985 PMCID: PMC3232021 DOI: 10.1016/j.neuron.2011.09.021] [Citation(s) in RCA: 306] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2011] [Indexed: 12/26/2022]
Abstract
Research in the fruit fly Drosophila melanogaster has led to insights in neural development, axon guidance, ion channel function, synaptic transmission, learning and memory, diurnal rhythmicity, and neural disease that have had broad implications for neuroscience. Drosophila is currently the eukaryotic model organism that permits the most sophisticated in vivo manipulations to address the function of neurons and neuronally expressed genes. Here, we summarize many of the techniques that help assess the role of specific neurons by labeling, removing, or altering their activity. We also survey genetic manipulations to identify and characterize neural genes by mutation, overexpression, and protein labeling. Here, we attempt to acquaint the reader with available options and contexts to apply these methods.
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Affiliation(s)
- Koen J.T. Venken
- Department of Molecular and Human Genetics, Neurological Research Institute, Baylor College of Medicine, Houston, Texas, 77030
| | - Julie H. Simpson
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, 20147
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Neurological Research Institute, Baylor College of Medicine, Houston, Texas, 77030
- Program in Developmental Biology, Department of Neuroscience, Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, 77030
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Bajaj K, Dewan PC, Chakrabarti P, Goswami D, Barua B, Baliga C, Varadarajan R. Structural correlates of the temperature sensitive phenotype derived from saturation mutagenesis studies of CcdB. Biochemistry 2009; 47:12964-73. [PMID: 19006334 DOI: 10.1021/bi8014345] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Temperature sensitive (ts) mutants are widely used to reversibly modulate protein function in vivo and to understand functions of essential genes. Despite this, little is known about the protein structural features and mechanisms responsible for generating a ts phenotype. Also, such mutants are often difficult to isolate, limiting their use. In this study, a library consisting of 75% of all possible single-site mutants of the 101-residue, homodimeric Escherichia coli toxin CcdB was constructed. Mutants were characterized in terms of their activity at two different temperatures and at six different expression levels. Of the total of 1430 single-site mutants that were screened, 231 (16%) mutants showed a ts phenotype. The bulk of these consisted of 120 ts mutants found at all 22 buried sites and 34 ts mutants at all seven active site residues involved in binding DNA gyrase. Of the remaining ts mutants, 16 were found at residues in van der Waals contact with active site residues, 36 were at partially buried residues, and 30 resulted from introduction of Pro. Thus virtually all ts mutants could be rationalized in terms of the structure of the native protein and without knowledge of folding pathways. Data were analyzed to obtain insights into molecular features responsible for the ts phenotype and to outline structure- and sequence-based criteria for designing ts mutants of any globular protein. The criteria were validated by successful prediction of ts mutants of three other unrelated proteins, TBP, T4 lysozyme, and Gal4.
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Affiliation(s)
- Kanika Bajaj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
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Chapter 3 Mapping and Manipulating Neural Circuits in the Fly Brain. ADVANCES IN GENETICS 2009; 65:79-143. [DOI: 10.1016/s0065-2660(09)65003-3] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Halpern ME, Rhee J, Goll MG, Akitake CM, Parsons M, Leach SD. Gal4/UAS transgenic tools and their application to zebrafish. Zebrafish 2008; 5:97-110. [PMID: 18554173 DOI: 10.1089/zeb.2008.0530] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The ability to regulate gene expression in a cell-specific and temporally restricted manner provides a powerful means to test gene function, bypass the action of lethal genes, label subsets of cells for developmental studies, monitor subcellular structures, and target tissues for selective ablation or physiological analyses. The galactose-inducible system of yeast, mediated by the transcriptional activator Gal4 and its consensus UAS binding site, has proven to be a highly successful and versatile system for controlling transcriptional activation in Drosophila. It has also been used effectively, albeit in a more limited manner, in the mouse. While zebrafish has lagged behind other model systems in the widespread application of Gal4 transgenic approaches to modulate gene activity during development, recent technological advances are permitting rapid progress. Here we review Gal4-regulated genetic tools and discuss how they have been used in zebrafish as well as their potential drawbacks. We describe some exciting new directions, in large part afforded by the Tol2 transposition system, that are generating valuable new Gal4/UAS reagents for zebrafish research.
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Molecular defects caused by temperature-sensitive mutations in Semliki Forest virus nsP1. J Virol 2008; 82:9236-44. [PMID: 18596091 DOI: 10.1128/jvi.00711-08] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alphavirus replicase protein nsP1 has multiple functions during viral RNA synthesis. It catalyzes methyltransferase and guanylyltransferase activities needed in viral mRNA capping, attaches the viral replication complex to cytoplasmic membranes, and is required for minus-strand RNA synthesis. Two temperature-sensitive (ts) mutations in Semliki Forest virus (SFV) were previously identified within nsP1: ts10 (E529D) and ts14 (D119N). Recombinant viruses containing these individual mutations reproduced the features of the original ts strains. We now find that the capping-associated enzymatic activities of recombinant nsP1, containing ts10 or ts14 lesions, were not ts. The mutant proteins and polyproteins also were membrane bound, mutant nsP1 interacted normally with the other nonstructural proteins, and there was no major defect in nonstructural polyprotein processing in the mutants, although ts14 surprisingly displayed slightly retarded processing. The two mutant viruses were specifically defective in minus-strand RNA synthesis at the restrictive temperature. Integrating data from SFV and Sindbis virus, we discuss the domain structure of nsP1 and the relative positioning of and interactions between the replicase proteins. nsP1 is suggested to contain a specific subdomain involved in minus-strand synthesis and interaction with the polymerase nsP4 and the protease nsP2.
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Current awareness on yeast. Yeast 2008. [DOI: 10.1002/yea.1457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Vector and parameters for targeted transgenic RNA interference in Drosophila melanogaster. Nat Methods 2007; 5:49-51. [PMID: 18084299 PMCID: PMC2290002 DOI: 10.1038/nmeth1146] [Citation(s) in RCA: 228] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2007] [Accepted: 11/16/2007] [Indexed: 11/09/2022]
Abstract
The conditional expression of hairpin constructs in Drosophila melanogaster has emerged in recent years as a method of choice in functional genomic studies. To date, upstream activating site-driven RNA interference constructs have been inserted into the genome randomly using P-element-mediated transformation, which can result in false negatives due to variable expression. To avoid this problem, we have developed a transgenic RNA interference vector based on the phiC31 site-specific integration method.
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