Analysis of copper-induced protein precipitation across the E. coli proteome

Abstract

Metal cations have been exploited for their precipitation properties in a wide variety of studies, ranging from differentiating proteins from serum and blood to identifying the protein targets of drugs. Despite widespread recognition of this phenomenon, the mechanisms of metal-induced protein aggregation have not been fully elucidated. Recent studies have suggested that Cu's ability to induce protein aggregation may be a main contributor to Cu-induced cell death. Here, we provide the first proteome-wide analysis of the relative sensitivities of proteins across the Escherichia coli proteome to Cu-induced aggregation. We utilize a Metal-induced Protein Precipitation methodology that relies on quantitative bottom-up proteomics to define the metal concentration-dependent precipitation properties of proteins on a proteomic scale. Our results establish that Cu far surpasses other metals in promoting protein aggregation and that the protein aggregation is reversible upon metal chelation. The bulk of the Cu bound in the protein aggregates is Cu1+, regardless of the Cu2+ source. Analysis of our Metal-induced Protein Precipitation data allows us to investigate underlying biophysical characteristics that determine a protein's sensitivity to Cu-induced aggregation, which is independent of the relative concentration of protein in the lysate. Overall, this analysis provides new insights into the mechanism behind Cu cytotoxicity, as well as metal cation induced protein aggregation.

Liquid–Liquid Phase Separation‐Mediated Photocatalytic Subcellular Hybrid System for Highly Efficient Hydrogen Production

“…All cells underwent uniform treatment conditions, the factor of protein misfolding and enrichment in E. coli caused by metal ions inducing bacterial oxidative stress was also ruled out. [ 55 , 56 ] Under bright‐field conditions, it was observed that the protein condensates compartmentalized the cytosolic of E. coli and exhibited localization with the fluorescence of QDs. Next, we used TEM to demonstrate from multiple perspectives that QDs synthesized in living cells spontaneously assemble with HM proteins at the two poles of bacteria to form subcellular compartments.…”

Glycyl-l-histidyl-l-lysine prevents copper- and zinc-induced protein aggregation and central nervous system cell death in vitro

“… 17 However, in cases of excess copper exposure, pathological binding can occur, leading to the formation of aggregates that primarily consist of proteins enriched in either cysteine or histidine. 18 , 19 In the case of cysteine-rich proteins, oxidative linking of cysteine-rich thiol groups together with intermolecular linkages by inner sphere electron transfer can lead to disulfide bridge formation between two proteins that persists even when copper is liberated. 20 In the case of amyloid beta (Aβ) (an example of a protein containing multiple histidine-binding sites), Cu + has been shown to accelerate Aβ 1 – 42 aggregation and Cu 2+ either enhances or inhibits Aβ species aggregation in a ratio- and pH-dependent manner.…”

“… 20 In the case of amyloid beta (Aβ) (an example of a protein containing multiple histidine-binding sites), Cu + has been shown to accelerate Aβ 1 – 42 aggregation and Cu 2+ either enhances or inhibits Aβ species aggregation in a ratio- and pH-dependent manner. 19 , 21 , 22 Furthermore, both ROS formation and oxidative bond formation are linked processes, as copper in conjunction with H 2 O 2 has been shown to enhance toxic Aβ dimer formation via dityrosine bridges between Aβ monomers in an oxidative process. 23 Similarly to copper, zinc is structurally significant with the ability to bind both histidine and cysteine, e.g.…”