Journal: Nature Communications
Article Title: Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo
doi: 10.1038/s41467-022-33951-0
Figure Lengend Snippet: a Experimental workflow for the XL-LC-MS/MS analysis of lysosome-enriched fractions. Created with BioRender.com. b Normalized β-hexosaminidase activities for individual fractions from lysosome enrichment by SPIONs. Data are presented as mean values + SD ( n = 3, biologically independent samples over three independent experiments). c Western blot analysis of lysosome-enriched fractions for contamination by other organelles ( n = 2). Lysosome: lysosomal proteins (CTSD, LAMP2, LIMP2, and LAMTOR1). Other: Golgi apparatus (GM130), cytoskeleton (TUBA), cytosol (GAPDH), endoplasmic reticulum (CANX), and mitochondria (SDHA). d Summed iBAQ abundances for proteins identified in lysosome-enriched fractions in ≥3 replicates. e Classification of unique cross-linked residue pairs. f Proteins detected in non-cross-linked lysosome-enriched fractions (proteome), and unique lysosomal cross-linked residue pairs (interactome) for DR and IT samples. g Localization of CSMs for 68 lysosomal proteins cross-linked in the DR and IT state. Cytosolic: proteins located at the cytosolic face of the lysosomal membrane; Lumen: lysosomal luminal proteins. h Correlation of cross-link identification and protein abundance for lysosomal proteins. CSMs and PSMs represent summed values of the analysis ( n = 6, biologically independent samples over six independent experiments (3× DR and 3× IT)). SPIONs superparamagnetic iron oxide nanoparticles, DR disrupted, IT intact, SCX strong cation-exchange, IN input, FT flow through, W wash, EL eluate, WCL whole-cell lysate, iBAQ intensity-based absolute quantification, XLs cross-links, CSMs cross-link spectral matches, PSMs peptide spectral matches. Source data are provided as a Source Data file.
Article Snippet: The following primary antibodies were used in this study: goat anti LIMP2 (Cat# AF1966-SP,1:2000), mouse anti ACT2 (Cat# A5316, 1:4000), and rabbit anti LAMTOR1 (Cat # HPA002997, 1:1000) from Sigma-Aldrich; mouse anti CANX (Cat# 66903-1-AP, 1:20,000), mouse anti FLOT2 (Cat# 66881-1-Ig, 1:1500), mouse anti FZD9 (Cat# 67023-1-Ig, 1:1500), rabbit anti ATP6V1D (Cat# 14920-1-AP, 1:1000), rabbit anti CTSD (Cat# # 21327-1-AP, 1:1000), rabbit anti FLOT1 (Cat# 15571-1-AP, 1:2000), rabbit anti GNB4 (Cat# 11978-2-AP, 1:2000), and rabbit anti SDHA (Cat# 14865-1-AP, 1:800) from Proteintech; goat anti LIMP2 (Cat# AF1966-SP, 1:2000) from R&D system; mouse anti ATP6V1B2 (Cat# SC166045, 1:1000) from Santa Cruz; mouse anti FLOT1 (Cat# 610821, 1:200), mouse anti FLOT2 (Cat# 610383, 1:200), and mouse anti GM130 (Cat# 610822) from BD Biosciences; mouse anti GAPDH (Cat# 5174, 1:2500), rabbit anti EEA1 (Cat# 2411, 1:200), rabbit anti FLOT1 (Cat# 18634, 1:200), and rabbit anti RRAGA (Cat# 4357, 1:1000) from Cell signaling; rabbit anti LPHN2 (Cat# NBP2-58704, 1:100) and rabbit anti LPHN3 (Cat# NLS1138, 1:200) from Novus Biologicals; goat anti-mouse IgG (H + L)-Alexa Fluor 488 (Cat# A-11029, 1:400), rabbit anti ATP6V1A1 (Cat# PA5-29191,1:2000), and rabbit anti LPHN1 (Cat # PA5-77475, 1:200) from Thermo Fisher Scientific; rabbit anti TUBA (Cat# 600-401-880, 1:2000) from Rockland; mouse anti LAMP2 (Cat# H4B4, 1:1000 for WB, 1:100 for IF) from Hybridoma Bank. rabbit anti DSSO (Self-made , 1:5000).
Techniques: Liquid Chromatography with Mass Spectroscopy, Western Blot, Residue, Membrane