Extended Data Fig. 6: Photo-affinity interaction mapping.

a, Western blots (10% SDS–PAGE gel, blotted to a PVDF membrane) of membrane protein extract from PAL-3- (4 mg l⁻¹), PAL-4- (10 mg l⁻¹) and PAL-7- (4 mg l⁻¹) labelled E. coli ATCC 25922 with chemiluminescence detection of biotinylated macromolecules. For gel source data, see Supplementary Fig. 1. b, Volcano plot showing relative abundance of proteins captured by streptavidin, and quantified by mass spectrometry, from E. coli cells photolabelled with PAL-7 versus control cells treated with 7 (n = 3 biologically independent samples each). Protein abundance changes (expressed in log₂) were calculated by linear mixed-effect model and tested for statistical significance using a two-sided t-test. P values obtained were further corrected for multiple comparisons using Benjamini–Hochberg method. Proteins are represented on the basis of the UniProt annotated subcellular ___location as dots (outer membrane) or crosses (no, or other, ___location); symbol size is scaled according to statistical significance. Significantly enriched proteins (abundance ratio ≥ 1.5 and adjusted P ≤ 0.05, shown as blue lines) are coloured in green. Outer membrane proteins that were also enriched in PAL-3 and PAL-4 photo-affinity interaction mapping experiments are highlighted. BamA is among the most significantly upregulated proteins, and is the only common outer membrane interaction candidate that was identified by all three photoprobes. A full list of proteins quantified by mass spectrometry in these experiments is supplied as Source Data

Source data.