Non-covalently bound cell surface proteins, including S-layer proteins (SLPs) and S-layer associated proteins (SLAPs) were extracted from the Lactobacillus strains using LiCl denaturing salt, as described previously (Johnson et al., 2013 (link)). SLP and SLAP pellets were resuspended in 10% (w/v) SDS (Fisher, Waltham, MA, USA). Proteins were quantified via bicinchoninic acid assay kit (Thermo Scientific, Waltham, MA, USA) and 10 ng was loaded and visualized via SDS-PAGE using precast 4–20% Precise Tris-HEPES protein gels (Thermo Scientific, Waltham, MA, USA). Gels were stained using AcquaStain (Bulldog Bio, Portsmouth, NH, USA) according to the instructions from the manufacturer.
Surface layer associated proteins extracted from the various L. acidophilus strains were identified using LC–MS/MS from the Genome Center Proteomics Core at the University of California, Davis, as described previously (Johnson et al., 2013 (link)). For all analyses, total spectral counts were utilized as a semi-quantitative indicator of protein abundance (Liu et al., 2004 (link)). Two-way clustering of total spectral counts was performed using JMP Genomics (version 5, SAS). Protein domains were identified for analysis using the Pfam protein family database (Finn et al., 2014 (link)).
Surface layer associated proteins extracted from the various L. acidophilus strains were identified using LC–MS/MS from the Genome Center Proteomics Core at the University of California, Davis, as described previously (Johnson et al., 2013 (link)). For all analyses, total spectral counts were utilized as a semi-quantitative indicator of protein abundance (Liu et al., 2004 (link)). Two-way clustering of total spectral counts was performed using JMP Genomics (version 5, SAS). Protein domains were identified for analysis using the Pfam protein family database (Finn et al., 2014 (link)).
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