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8 protocols using gfp rab5

1

EPEC Strain and Recombinant Protein Protocols

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EPEC E2348 strain was kindly provided by Professor Gad Frankel, Imperial College London, UK. Rab5-GFP, Rab7-GFP, and Rab9-GFP, Rab5-DN-mCherry and Rab7-DN-mCherry were from Addgene. VSVG3-SP-GFP was kindly provided by Associate Professor Derek Toomre, Yale University, USA. The plasmid encoding Exo70-GFP was kindly provided by Team Leader Philippe Chavrier, Institut Curie, France. The plasmid encoding TfR-mCherry was kindly provided by Assistant Professor Matthew Kennedy, UC Denver, Colorado, USA. EPEC bacteria expressing GFP were produced by transformation of a GFP plasmid (GFP inserted into the pBluescript SK+ vector, kindly provided by Dr. Stefanie Bechstein, iNANO, AU, DK) into the EPEC E2348 strain and selected with 100 mg/L ampicillin. Before transformation, EPEC bacteria were made competent through a series of resuspensions in 10% glycerol using decreasing volumes after every spin.
Anti-gp135 mAb, clone 3F2/DB [70 (link)], kindly provided by Professor W. James Nelson, Stanford University, California, USA, was used as undiluted hybridoma supernatant. Antibodies against Lipid A were purchased from Abcam.
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2

Generating SPC99 Mutant Constructs

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The pcDNA3 SPC99G33L construct was generated using the QuickChange II Site-Directed Mutagenesis Kit (Agilent Technologies) with pcDNA3 SPC99 previously described (flammang 2012) and appropriated primers: 5′- AAG GCG CAA TCA TTC TAC TCA TGG TGG GCG GTG - 3′ and 5′- CAC CGC CCA CCA TGA GTA GAA TGA TTG CGC CTT - 3′. The pcDNA3 SPC99G29L/G33L plasmid was obtained using the same protocol with the pcDNA3 SPC99G33L previously generated and the following primers: 5′- GGG TTC AAA CAA ACT CGC AAT CAT TCT ACT C - 3′ and 5′ - GAG TAG AAT GAT TGC GAG TTT GTT TGA ACC C - 3′). The doxycyclin-inductible pSBtet SPC99 construct used for stable cell line generation was obtained as following. First, the SPC99 fragment was amplified by PCR from the pcDNA3 SPC99 using the following primers (5′– ATA TTA GGC CTC TGA GGC CCC ACC ATG CTG CCC GGT TTG GCA C – 3′ and 5′– GAT GGC CTG ACA GGC CCT AGT TCT GCA TCT GCT CAA AGA ACT TG TAG GTT – 3′) to introduce the SfiI restriction site at both 5′ and 3′ end of fragment. The resulting product was then digested by SfiI and subcloned into the pSBtet vector. All constructs were verified by sequencing. Rab5-GFP, Rab7-GFP and Lamp1-GFP were from Addgene and the SorLAmyc construct was a kind gift from Peter St-George-Hyslop.
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3

OSBPL2 Cloning and Mutagenesis Protocol

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cDNA of human OSBPL2 was purchased from OriGene Technologies (RC201344) and subcloned into the pENTR-D-TOPO vector (Invitrogen, K240020). Expression vectors were constructed using LR clonase (Invitrogen, 11,791,019) following the manufacturer’s instructions, with a MYC- or FLAG-tag at the N terminus. OSBPL2 mutant clones were generated via PCR-based site-directed mutagenesis using the Quick Change II XL site-directed mutagenesis kit (Agilent Technologies, 200,521). In addition, OSBPL2 cDNA was cloned into p3XFLAG-CMV™-10 (Sigma, E7658) and pCAGGS (RDB08938, Riken). SQSTM1/p62 plasmids were kindly provided by Dr Yong Tae Kwon (College of Medicine, Seoul National University). The following vectors were used: p3XFLAG-CMV™-7 (Sigma, E7408), pEYFP-Golgi (Clontech, 6909–1), pEYFP-ER (Clontech, 6906–1), pCAG-mGFP-Membrane (Addgene, 14,757; deposited by Connie Cepko), GFP-RAB5 (Addgene, 31,733; deposited by Ron Vale), and GFP-LAMP1 (Addgene, 16,290; deposited by Ron Vale).
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4

Early Endosome and Lysosome Imaging

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HEK293 cells were seeded in 35 mm glass bottom dishes (Fisher Scientific) for a confluency of approximately 70% at the time of transfection. For early endosome morphology and population experiments, a transfection mixture of 1 μg GFP-Rab5 (Addgene # 61802), 7.5 μL Mirus transfection reagent TransIT LT1, and 250 μL Opti-MEM was used. For lysosome morphology and population experiments, a transfection mixture of 750 ng mCherry-Lysosomes-20 (Addgene plasmid #55073), 7.5 μL Mirus transfection reagent TransIT LT1, and 100 μL OPTIMEM was used. The morning following the transfection, cells were switched into DMEM+10% FBS and drugged accordingly with a final DMSO concentration of 0.15%. Drugs were incubated with cells for 3 hours at 37°C, 5% CO2. Hoechst 3342 nuclear stain diluted in PBS was added to cells for a final concentration of 1:10,000 and incubated for the final 20 minutes of drug treatment. After treatment, cells were fixed in 1 mL 4% PFA for 10 minutes at room temperature followed by washing with ice cold PBS. Fixed samples were stored in PBS at 4°C until imaging. Three biological replicates were performed on different days.
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5

Multimodal Subcellular Imaging Techniques

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The plasmids to fluorescently label the cell membrane (pYFP-Mem), the endoplasmic reticulum (pYFP-ER), mitochondria (pYFP-mito) and peroxisomes (pEGFP-Pex) were obtained from Clontech. The plasmid to label the endosomes (GFP-Rab5; Addgene plasmid # 31733) was a gift from Richard Pagano (Choudhury et al., 2002 (link)). Lysosomes were counterstained with LysoTracker (Thermo Scientific). The golgi apparatus was counterstained using antibodies directed against cis golgi marker GM-130 (sc-55591, Santa Cruz) and trans-golgi marker TGN38 (sc-166594, Santa Cruz).
Co-localization was observed using Zeiss LSM 510 Meta system. Quantitative analysis of co-localization was carried out by calculating Pearson’s correlation coefficients using LSM 510 software.
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6

Visualizing Endosome and Lysosome Dynamics

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HEK293 cells were
seeded in 35 mm glass-bottom dishes (Fisher Scientific)
for a confluency of approximately 70% at the time of transfection.
For early endosome morphology and population experiments, a transfection
mixture of 1 μg of GFP-Rab5 (Addgene # 61802), 7.5 μL
of Mirus transfection reagent TransIT LT1, and 250 μL of Opti-MEM
was used. For lysosome morphology and population experiments, a transfection
mixture of 750 ng of mCherry-Lysosomes-20 (Addgene plasmid #55073),
7.5 μL of Mirus transfection reagent TransIT LT1, and 100 μL
of Opti-MEM was used. The morning following the transfection, cells
were switched into DMEM+10% FBS and drugged accordingly with a final
DMSO concentration of 0.15%. Drugs were incubated with cells for 3
h at 37 °C, 5% CO2. Hoechst 33342 nuclear stain diluted
in PBS was added to cells for a final concentration of 1:10,000 and
incubated for the final 20 min of drug treatment. After treatment,
cells were fixed in 1 mL 4% PFA for 10 min at room temperature followed
by washing with ice-cold PBS. Fixed samples were stored in PBS at
4 °C until imaging. Three biological replicates were performed
on different days.
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7

Visualizing Phosphoinositide Dynamics

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All salts were from Sigma-Aldrich. PAO was from Sigma-Aldrich, and wortmannin and PIK93 were from TOCRIS Bioscience. The following plasmids were used: GFP-PH-OSBP (Balla et al., 2005 (link); gift from Tamas Balla, National Institutes of Health, Bethesda, MD), GFP-PHx2-OSH2 (Stefan et al., 2011 (link); plasmid 36095; Addgene), GFP-P4M-SidM (Hammond et al., 2014 (link); plasmid 51472; Addgene), mRFP-PH-PLCδ1, mRFP-PH-Akt, GFP-Sac2 (Nakatsu et al., 2015 (link); gift from Pietro DeCamilli, Yale University, New Haven, CT), GFP-Rab27a, GFP-Rab3a, NPY-GFP, NPY-mCherry, VAMP2-pHluorin (all gifts from Sebastian Barg, Uppsala University, Uppsala, Sweden), Lamp1-RFP (Sherer et al., 2003 (link); plasmid 1817; Addgene), GFP-Rab5, GFP-EEA1 (gifts from Pietro DeCamilli), CIBN-CAAX (Idevall-Hagren et al., 2012 (link)), GFP-CRY2-5ptaseOCRL (Idevall-Hagren et al., 2012 (link)), GFP-CRY2-iSH2 (Idevall-Hagren et al., 2012 (link)), R-GECO1 (Zhao et al., 2011 (link); plasmid 32444; Addgene), GFP-Lact-C2 (Yeung et al., 2008 (link); plasmid 22853; Addgene), EGFP-Rab4a (Rzomp et al., 2003 (link); plasmid 49434; Addgene), GFP-Rab10 (Huckaba et al., 2011 (link); plasmid 31737; Addgene), Granuphilin-GFP (Gálvez-Santisteban et al., 2012 (link); plasmid 40032; Addgene), and GFP-2xFYVEEEA1 (Petiot et al., 2003 (link)).
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8

Fluorescent Labeling of Organelles

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The plasmids to fluorescently label the cell membrane (pYFP-Mem), the ER (pYFP-ER), mitochondria (pYFP-mito) and peroxisomes (pEGFP-Pex) were obtained from Clontech. The plasmid to label the endosomes (GFP-Rab5; Addgene plasmid # 31733) was a gift from Richard Pagano (Choudhury et al., 2002 (link)). Lysosomes were counterstained with Lamp1-GFP.
Co-localization was observed using Zeiss LSM 510 Meta system. Quantitative analysis of co-localization was carried out by calculating Pearson’s correlation coefficients using LSM 510 software.
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