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3 protocols using octa probe d 8

1

Molecular Signaling Pathway Profiling

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All common chemicals were obtained from Sigma-Aldrich (Wicklow, Ireland) unless otherwise stated. Antibodies used for Western blot and co-immunoprecipitation include rabbit anti-Bid (Abcam, ab62469, 1:1000), rabbit anti-Peli1 (Abcam ab199336, 1:1000), rabbit anti-TRAF3 (Abcam, ab76147, 1:500), mouse anti-TRAF6 (Santa Cruz, sc8409, 1:200), rabbit anti-phospho-IRF3 (Cell Signaling, 4947P, 1:500), rabbit anti-phospho-TBK1 (Cell Signaling, 5483P, 1:500), rabbit anti-phospho c-Jun (Cell Signaling, 9261S, 1:1000), rabbit anti-A20/TNFAIP3 (Cell Signaling, 5630, 1:1000), rabbit anti-LC3 (Abcam, ab51520, 1:2000), rabbit anti-FLAG (OctA-Probe D-8, Santa Cruz, sc-807, 1:500), anti- α-Tubulin (Sigma-Aldrich, T6199, 1:5000), anti-β-Actin (Sigma-Aldrich, A3853, 1:5000), and anti-GAPDH (Abcam, ab8245-100,1:5000). Bortezomib was obtained from Millennium Pharmaceuticals (Cambridge, MA, USA). Lipopolysaccharide (LPS) was obtained from (Sigma-Aldrich, L4391), and PolyI:C (31852-29-6) and Pam3CSK4 (112208-00-1) were obtained from InvivoGen.
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2

Western Blot Analysis of PIF4-FLASH and PIF5-FLASH

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Entire PIF4-FLASH and PIF5-FLASH seedlings were grown in the indicated conditions and samples were harvested at ZT12 and ZT16 on day 14 of the experiment. After pulverizing the tissue as described above, whole-cell extracts were prepared by the hot extraction method described previously (Al-Sady et al., 2006 (link)), except the protease inhibitor mix was the cOmplete, EDTA-free Protease Inhibitor Cocktail (Roche Applied Science, www.roche-applied-science.com). Proteins were separated on 10% SDS–polyacrylamide gels and western blotting was performed as described previously (Harmon et al., 2008 (link)). Proteins with the FLASH epitope were detected with an equal mix of OctA-probe (D-8) and c-Myc (A-14) antisera (Santa Cruz Biotechnology, www.scbt.com) as primary antibodies, followed by goat anti-rabbit IgG–horseradish peroxidase (HRP) conjugate (Santa Cruz Biotechnology, www.scbt.com) as the secondary antibody.
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3

SDS-PAGE and Western Blot Analysis

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Sample preparation for SDS-PAGE was performed by adding Laemmli Sample Buffer. Protein samples were heated at 70 C for 7 min, subjected to 8% polyacrylamide gel electrophoresis and transferred to polyvinylidene fluoride (PVDF) Immobilon-P membrane (Millipore) by the semi-dry transfer system (Bio-Rad). Membranes were blocked with 5% non-fat dry milk in TBST for 60 min and then incubated with rabbit polyclonal primary antibodies diluted as follows, 1:100 OctA-Probe (D-8), 1:2000 anti-GFP (Santa Cruz Biotechnology), 1:1000 anti-GFP (Cell Signaling Technology) used for immunoblots of Figure S2, 1:3000 anti-D1 (Zhang et al., 2000) , 1:3000 anti-CYTF (Alt et al., 1983) , 1:10000 anti-CYTB6/F (Alt et al., 1983) , 1:3000 anti-LHCP (Adamska et al., 2001) and 1:700 anti-CP (Barbato et al., 1992) . Immunoblotting of co-immunoprecipitation experiments performed with mouse monoclonal OctA-Probe (H-5) (Santa Cruz Biotechnology) in 1:500 dilution. After three washes with TBST, the blots were incubated with 1:10000 diluted goat anti-rabbit IgG-HRP or 1:3000 diluted goat anti-mouse IgG-HRP secondary antibody (Santa Cruz Biotechnology). Western blot detection was performed with chemiluminescence luminol reagent (Santa Cruz Biotechnology) by exposure to UltraCruz blue autoradiography film. Western blots were performed in triplicates.
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