scholarly journals Tissue-specific tagging of endogenous loci inDrosophila melanogaster

2015 ◽  
Author(s):  
Kate Koles ◽  
Anna R Yeh ◽  
Avital A Rodal
Keyword(s):  
Protein Function ◽  
Fluorescent Protein ◽  
Endocytic Pathway ◽  
Expression Systems ◽  
Tissue Specific ◽  
Efficient Gene ◽  
Endogenous Protein ◽  
Endogenous Proteins ◽  
Endogenous Loci ◽  
Fluorescent Protein Tags

Fluorescent protein tags have revolutionized cell and developmental biology, and in combination with binary expression systems they enable diverse tissue-specific studies of protein function. However these binary expression systems often do not recapitulate endogenous protein expression levels, localization, binding partners, and developmental windows of gene expression. To address these limitations, we have developed a method called T-STEP (Tissue-SpecificTagging ofEndogenousProteins) that allows endogenous loci to be tagged in a tissue specific manner. T-STEP uses a combination of efficient gene targeting and tissue-specific recombinase-mediated tag swapping to temporally and spatially label endogenous proteins. We have employed this method to GFP tag OCRL (a phosphoinositide-5-phosphatase in the endocytic pathway) and Vps35 (a Parkinson’s disease-implicated component of the endosomal retromer complex) in diverse Drosophila tissues including neurons, glia, muscles, and hemocytes. Selective tagging of endogenous proteins allows for the first time cell type-specific live imaging and proteomics in complex tissues.

scholarly journals Split-wrmScarlet and split-sfGFP: Tools for faster, easier fluorescent l abeling of endogenous proteins in Caenorhabditis elegans

Genetics ◽  
2021 ◽  
Author(s):  
Jérôme Goudeau ◽  
Catherine S Sharp ◽  
Jonathan Paw ◽  
Laura Savy ◽  
Manuel D Leonetti ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Fluorescent Proteins ◽  
Fluorescent Labeling ◽  
Large Fragment ◽  
C Elegans ◽  
High Affinity ◽  
Red Fluorescent Proteins ◽  
Invaluable Tool ◽  
Endogenous Proteins ◽  
Fluorescent Tags

Abstract We create and share a new red fluorophore, along with a set of strains, reagents and protocols, to make it faster and easier to label endogenous C. elegans proteins with fluorescent tags. CRISPR-mediated fluorescent labeling of C. elegans proteins is an invaluable tool, but it is much more difficult to insert fluorophore-size DNA segments than it is to make small gene edits. In principle, high-affinity asymmetrically split fluorescent proteins solve this problem in C. elegans: the small fragment can quickly and easily be fused to almost any protein of interest, and can be detected wherever the large fragment is expressed and complemented. However, there is currently only one available strain stably expressing the large fragment of a split fluorescent protein, restricting this solution to a single tissue (the germline) in the highly autofluorescent green channel. No available C. elegans lines express unbound large fragments of split red fluorescent proteins, and even state-of-the-art split red fluorescent proteins are dim compared to the canonical split-sfGFP protein. In this study, we engineer a bright, high-affinity new split red fluorophore, split-wrmScarlet. We generate transgenic C. elegans lines to allow easy single-color labeling in muscle or germline cells and dual-color labeling in somatic cells. We also describe a novel expression strategy for the germline, where traditional expression strategies struggle. We validate these strains by targeting split-wrmScarlet to several genes whose products label distinct organelles, and we provide a protocol for easy, cloning-free CRISPR/Cas9 editing. As the collection of split-FP strains for labeling in different tissues or organelles expands, we will post updates at doi.org/10.5281/zenodo.3993663

Rab22a affects the morphology and function of the endocytic pathway

2001 ◽  
Vol 114 (22) ◽  
pp. 4041-4049 ◽  
Author(s):  
Rosana Mesa ◽  
Cristina Salomón ◽  
Marcelo Roggero ◽  
Philip D. Stahl ◽  
Luis S. Mayorga
Keyword(s):  
Fluorescent Protein ◽  
Fluid Phase ◽  
Small Gtpases ◽  
Endocytic Pathway ◽  
Site Directed Mutagenesis ◽  
Rab Proteins ◽  
Rab Protein ◽  
Late Endosomes ◽  
And Function ◽  
Negative Mutant

Soon after endocytosis, internalized material is sorted along different pathways in a process that requires the coordinated activity of several Rab proteins. Although abundant information is available about the subcellular distribution and function of some of the endocytosis-specific Rabs (e.g. Rab5 and Rab4), very little is known about some other members of this family of proteins. To unveil some of the properties of Rab22a, one of the less studied endosome-associated small GTPases, we have expressed the protein tagged with the green fluorescent protein in CHO cells. The results indicate that Rab22a associates with early and late endosomes (labeled by a 5 minute rhodamine-transferrin uptake and the cation-independent mannose 6-phosphate receptor, respectively) but not with lysosomes (labeled by 1 hour rhodamine horseradish peroxidase uptake followed by 1 hour chase). Overexpression of the protein causes a prominent morphological enlargement of the early and late endosomes. Two mutants were generated by site-directed mutagenesis, a negative mutant (Rab22aS19N, with reduced affinity for GTP) and a constitutively active mutant (Rab22aQ64L, with reduced endogenous GTPase activity). The distribution of the negative mutant was mostly cytosolic, whereas the positive mutant associated with early and late endosomes and, interestingly also with lysosomes and autophagosomes (labeled with monodansylcadaverine). Cells expressing Rab22a wild type and Rab22aS19N displayed decreased endocytosis of a fluid phase marker. Conversely, overexpression of Rab22aQ64L, which strongly affects the morphology of endosomes, did not inhibit bulk endocytosis. Our results show that Rab22a has a unique distribution along the endocytic pathway that is not shared by any other Rab protein, and that it strongly affects the morphology and function of endosomes.

The Effect of Fluorescent Protein Tags on Phosphoglycerate Kinase Stability Is Nonadditive

2016 ◽  
Vol 120 (11) ◽  
pp. 2878-2885 ◽  
Author(s):  
Kapil Dave ◽  
Hannah Gelman ◽  
Chu Thi Hien Thu ◽  
Drishti Guin ◽  
Martin Gruebele
Keyword(s):  
Fluorescent Protein ◽  
Phosphoglycerate Kinase ◽  
Fluorescent Protein Tags ◽  
Protein Tags

scholarly journals Compensatory Link between Fusion and Endocytosis of Human Immunodeficiency Virus Type 1 in Human CD4 T Lymphocytes

2004 ◽  
Vol 78 (3) ◽  
pp. 1375-1383 ◽  
Author(s):  
Evelyne Schaeffer ◽  
Vanessa B. Soros ◽  
Warner C. Greene
Keyword(s):  
Human Immunodeficiency Virus ◽  
Mononuclear Cells ◽  
Fluorescent Protein ◽  
Reciprocal Relationship ◽  
Endocytic Pathway ◽  
Productive Infection ◽  
Target Cells ◽  
Concanamycin A ◽  
Immunodeficiency Virus

ABSTRACT Virions of the type 1 human immunodeficiency virus (HIV-1) can enter target cells by fusion or endocytosis, with sharply different functional consequences. Fusion promotes productive infection of the target cell, while endocytosis generally leads to virion inactivation in acidified endosomes or degradation in lysosomes. Virion fusion and endocytosis occur equally in T cells, but these pathways have been regarded as independent because endocytosis of HIV virions requires neither CD4 nor CCR5/CXCR4 engagement in HeLa-CD4 cells. Using flow cytometric techniques to assess the binding and entry of green fluorescent protein (GFP)-Vpr-labeled HIV virions into primary peripheral blood mononuclear cells, we have found that HIV fusion and endocytosis are restricted to the CD4-expressing subset of cells and that both pathways commonly require the initial binding of HIV virions to surface CD4 receptors. Blockade of CXCR4-tropic HIV virion fusion with AMD3100, a CXCR4-specific entry inhibitor, increased virion entry via the endocytic pathway. Similarly, inhibition of endosome acidification with bafilomycin A1, concanamycin A, or NH4Cl enhanced entry via the fusion pathway. Although fusion remained dependent on CD4 and chemokine receptor binding, the endosome inhibitors did not alter surface expression of CD4 and CXCR4. These results suggest that fusion in the presence of the endosome inhibitors likely occurs within nonacidified endosomes. However, the ability of these inhibitors to impair vesicle trafficking from early to late endosomes in some cells could also increase the recycling of these virion-containing endosomes to the cell surface, where fusion occurs. In summary, our results reveal an unexpected, CD4-mediated reciprocal relationship between the pathways governing HIV virion fusion and endocytosis.

scholarly journals Visualization of Intracellular Transport of Vesicular Stomatitis Virus Nucleocapsids in Living Cells

2006 ◽  
Vol 80 (13) ◽  
pp. 6368-6377 ◽  
Author(s):  
Subash C. Das ◽  
Debasis Nayak ◽  
You Zhou ◽  
Asit K. Pattnaik
Keyword(s):  
Vesicular Stomatitis Virus ◽  
Protein Function ◽  
Intracellular Transport ◽  
Fluorescent Protein ◽  
De Novo ◽  
Virus Production ◽  
Hinge Region ◽  
Cell Periphery ◽  
P Protein ◽  
Vesicular Stomatitis

ABSTRACT The phosphoprotein (P) of vesicular stomatitis virus (VSV) is a subunit of the viral RNA polymerase. In previous studies, we demonstrated that insertion of 19 amino acids in the hinge region of the protein had no significant effect on P protein function. In the present study, we inserted full-length enhanced green fluorescent protein (eGFP) in frame into the hinge region of P and show that the fusion protein (PeGFP) is functional in viral genome transcription and replication, albeit with reduced activity. A recombinant vesicular stomatitis virus encoding PeGFP in place of the P protein (VSV-PeGFP), which possessed reduced growth kinetics compared to the wild-type VSV, was recovered. Using the recombinant VSV-PeGFP, we show that the viral replication proteins and the de novo-synthesized RNA colocalize to sites throughout the cytoplasm, indicating that replication and transcription are not confined to any particular region of the cytoplasm. Real-time imaging of the cells infected with the eGFP-tagged virus revealed that, following synthesis, the nucleocapsids are transported toward the cell periphery via a microtubule (MT)-mediated process, and the nucleocapsids were seen to be closely associated with mitochondria. Treatment of cells with nocodazole or Colcemid, drugs known to inhibit MT polymerization, resulted in accumulation of the nucleocapsids around the nucleus and also led to inhibition of infectious-virus production. These findings are compatible with a model in which the progeny viral nucleocapsids are transported toward the cell periphery by MT and the transport may be facilitated by mitochondria.

scholarly journals Tissue-specific tagging of endogenous loci inDrosophila melanogaster

Biology Open ◽  
2015 ◽  
Vol 5 (1) ◽  
pp. 83-89 ◽  
Author(s):  
Kate Koles ◽  
Anna R. Yeh ◽  
Avital A. Rodal
Keyword(s):  
Tissue Specific ◽  
Endogenous Loci

scholarly journals Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering

2017 ◽  
Author(s):  
Sean A. Higgins ◽  
Sorel Ouonkap ◽  
David F. Savage
Keyword(s):  
Structure Function ◽  
Sequence Space ◽  
Protein Function ◽  
Fluorescent Protein ◽  
One Pot ◽  
Protein Mutagenesis ◽  
Protein Mutants ◽  
Protein Libraries

ABSTRACTComprehensive and programmable protein mutagenesis is critical for understanding structure-function relationships and improving protein function. However, current techniques enabling comprehensive protein mutagenesis are based on PCR and require in vitro reactions involving specialized protocols and reagents. This has complicated efforts to rapidly and reliably produce desired comprehensive protein libraries. Here we demonstrate that plasmid recombineering is a simple and robust in vivo method for the generation of protein mutants for both comprehensive library generation as well as programmable targeting of sequence space. Using the fluorescent protein iLOV as a model target, we build a complete mutagenesis library and find it to be specific and unbiased, detecting 99.8% of our intended mutations. We then develop a thermostability screen and utilize our comprehensive mutation data to rapidly construct a targeted and multiplexed library that identifies significantly improved variants, thus demonstrating rapid protein engineering in a simple one-pot protocol.

scholarly journals Mitotic Golgi clusters are not tubular endosomes

1993 ◽  
Vol 104 (3) ◽  
pp. 811-818 ◽  
Author(s):  
M. Pypaert ◽  
T. Nilsson ◽  
E.G. Berger ◽  
G. Warren
Keyword(s):  
Hela Cell ◽  
Endocytic Pathway ◽  
Hela Cell Line ◽  
Frozen Sections ◽  
Qualitative And Quantitative ◽  
Quantitative Studies ◽  
Cell Biol ◽  
Endogenous Protein ◽  
Secondary Antibodies ◽  
Two Populations

HeLa cells were incubated with 15 nm BSA-gold for 1 or 2 hours to mark the endocytic pathway and mitotic cells were then isolated by shake-off. Thin, frozen sections were labelled with antibodies against two resident Golgi markers, beta-(1,4)-galactosyltransferase and N-acetylglucosaminyltransferase I. Detection of the latter was aided by the use of a HeLa cell line stably expressing a myc-tagged version of the endogenous protein. The secondary antibodies were coupled to either 5 or 10 nm gold so that the distribution of each of the three markers could be followed. Qualitative and quantitative studies showed that there were two populations of clusters, those described by us earlier and termed Golgi clusters (Lucocq et al. (1987) J. Cell Biol. 104, 865–874), containing either or both Golgi markers, and clusters of tubular endosomes containing BSA-gold. There was very little overlap showing that Golgi clusters cannot be tubular endosomes as concluded by Tooze and Hollinshead (1992) Eur. J. Cell Biol. 58, 228–242.

scholarly journals Optimal fluorescent protein tags for quantifying protein oligomerization in living cells

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Valentin Dunsing ◽  
Madlen Luckner ◽  
Boris Zühlke ◽  
Roberto A. Petazzi ◽  
Andreas Herrmann ◽  
...  
Keyword(s):  
Fluorescent Protein ◽  
Living Cells ◽  
Protein Oligomerization ◽  
Fluorescent Protein Tags ◽  
Protein Tags

scholarly journals Microhomology-based CRISPR tagging tools for protein tracking, purification, and depletion

2019 ◽  
Vol 294 (28) ◽  
pp. 10877-10885 ◽  
Author(s):  
Da-Wei Lin ◽  
Benjamin P. Chung ◽  
Jia-Wei Huang ◽  
Xiaorong Wang ◽  
Lan Huang ◽  
...  
Keyword(s):  
Protein Function ◽  
Mammalian Cells ◽  
Gene Locus ◽  
End Joining ◽  
High Quality ◽  
Physiological Conditions ◽  
Protein Tracking ◽  
Endogenous Proteins ◽  
And Behavior ◽  
Fluorescence Tags

Work in yeast models has benefitted tremendously from the insertion of epitope or fluorescence tags at the native gene locus to study protein function and behavior under physiological conditions. In contrast, work in mammalian cells largely relies on overexpression of tagged proteins because high-quality antibodies are only available for a fraction of the mammalian proteome. CRISPR/Cas9-mediated genome editing has recently emerged as a powerful genome-modifying tool that can also be exploited to insert various tags and fluorophores at gene loci to study the physiological behavior of proteins in most organisms, including mammals. Here we describe a versatile toolset for rapid tagging of endogenous proteins. The strategy utilizes CRISPR/Cas9 and microhomology-mediated end joining repair for efficient tagging. We provide tools to insert 3×HA, His6FLAG, His6-Biotin-TEV-RGSHis6, mCherry, GFP, and the auxin-inducible degron tag for compound-induced protein depletion. This approach and the developed tools should greatly facilitate functional analysis of proteins in their native environment.

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