Yoshikatsu Kanai

Proteases play crucial roles in numerous biological processes through specific protein cleavage, and their dysregulation has been implicated in various diseases. To better understand protease specificity, we developed a lauroylation-assisted proteomic identification of protease cleavage sites (PICS) workflow that labels and enriches targeted protease-generated neo-N-termini using economical reagents and standard laboratory equipment. The lauroylation enables both discrimination of the neo-N-termini in LC-MS/MS and efficient enrichment on a C18 StageTip by exploiting its hydrophobicity. Among tested acylations, we found lauroylation to be optimal for PICS and improved enrichment and fractionation conditions. We demonstrated that this method can profile specificities of multiple proteases with high sensitivity. Furthermore, we extended this concept to N-terminomics to examine proteolysis at the protein level. Protein N-terminal dimethylation is used for labeling, and tryptic internal peptides are lauroylated for removal. This approach identified over 1500 cleavages induced by etoposide, including 912 Asp-cleaved sites consistent with caspase-3 motifs and sensitive to inhibition by Z-DEVD-FMK. Additionally, 2286 protein N-termini were identified in untreated cells, including 1794 non-ORF N-termini with 665 previously annotated processing sites. These results demonstrate that our workflow provides a simple, economical, and widely applicable method for characterizing protease cleavage at both peptide and protein levels.

Bacteria reduce toxic selenium oxyanions, such as selenite, to elemental selenium (Se0), forming selenium nanoparticles (SeNPs) either intracellularly or extracellularly. However, the mechanism through which extracellular SeNPs (Ex-SeNPs) are exported remains unclear. In this study, we characterized Ex-SeNPs biosynthesized by Escherichia coli during the aerobic reduction of selenite. The SeNPs appeared within 2 h of exposure, remained extracellular, and displayed a consistent spherical morphology (∼100 nm). Purified Ex-SeNPs consisted of an Se0 core enveloped by a membrane-like layer containing lipids, proteins, carbohydrates, peptidoglycan, and lipopolysaccharides. Fluorescence microscopy and gas chromatography-mass spectrometry indicated that the encapsulated membrane originates from the E. coli cell membrane. Notably, mutants deficient in the outer membrane proteins OmpC or TolA failed to excrete SeNPs, resulting in intracellular accumulation despite efficient Se0 synthesis. Our findings suggest that E. coli forms SeNPs intracellularly and exports them via an envelope-dependent process, during which the particles may become encapsulated in membrane-like structures. These findings help clarify the mechanism underlying a membrane-dependent pathway for SeNP detoxification and export that had been suggested but not directly demonstrated.