Aggregating sequences that occur in many proteins constitute weak spots of bacterial proteostasis

Abstract

Aggregation is a sequence-specific process, nucleated by short aggregation-prone regions (APRs) that can be exploited to induce aggregation of proteins containing the same APR. Here, we find that most APRs are unique within a proteome, but that a small minority of APRs occur in many proteins. When aggregation is nucleated in bacteria by such frequently occurring APRs, it leads to massive and lethal inclusion body formation containing a large number of proteins. Buildup of bacterial resistance against these peptides is slow. In addition, the approach is effective against drug-resistant clinical isolates of Escherichia coli and Acinetobacter baumannii, reducing bacterial load in a murine bladder infection model. Our results indicate that redundant APRs are weak points of bacterial protein homeostasis and that targeting these may be an attractive antibacterial strategy.

Designer Amyloid Cell-Penetrating Peptides for Potential Use as Gene Transfer Vehicles

“…They were also found to be lethal to bacterial cells [14,15]. Their specific toxicity toward bacterial and not mammalian cells involves uptake mechanisms and specific cross-aggregation with bacterial homologous sequences; this cross-aggregation subsequently leads to disruption of bacterial protein homeostasis as a result of the accumulation of protein aggregates [14,15]. Elucidating the mechanism of antimicrobial action of the two peptides reported here will be the subject of future studies.…”

“…Cationic aggregating peptides comprising arginine residues, as well as short aggregation-prone residue stretches, were recently identified via bioinformatics approaches in the bacterial proteome and were reported to internalize in mammalian cells. They were also found to be lethal to bacterial cells [14,15]. Their specific toxicity toward bacterial and not mammalian cells involves uptake mechanisms and specific cross-aggregation with bacterial homologous sequences; this cross-aggregation subsequently leads to disruption of bacterial protein homeostasis as a result of the accumulation of protein aggregates [14,15].…”

“…Elucidating the mechanism of antimicrobial action of the two peptides reported here will be the subject of future studies. It did not escape our attention that the quasi-homologous sequence SAIIGI was identified with a high cross-aggregation score with E. coli proteins in Reference [14], and the designed RSAIIGIIRRPRSAIIGIIRR sequence was predicted to have antibacterial action [14]. It is plausible to hypothesize that the antibacterial activity of the two peptides reported here could follow the same mechanism as that reported in Reference [14], i.e., a cell-penetrating activity mediated by positively charged residues and cross-interaction of the amyloid cores with bacterial sequences, leading to aggregates that disrupt bacterial proteostasis.…”

“…These nanosized particles can be exploited for the targeted delivery of both nucleic acids and protein drugs. Very recently, a novel category of promising AMPs was reported, based on a number of bacterial aggregation-prone regions (APRs) which are not toxic to mammalian cells but can induce protein aggregation in the bacterial cell, leading to loss of the bacterial proteostasis and eventual bacterial cell death [14,15]. It seems, therefore, that properly designed protein and peptide aggregates in either synthetic or recombinant form could be amenable to rational design targeting cell penetration and drug or DNA delivery.…”

Entropic Bristles Tune the Seeding Efficiency of Prion-Nucleating Fragments

“…Conversely, it has also been shown that the introduction of point mutations that abolish the aggregation propensity of an APR is sufficient to reduce the aggregation propensity of the entire protein (Ganesan et al, 2016;Marshall et al, 2016). Finally, short peptides solely coding for such APRs are able to induce the aggregation of a full-length protein comprising that APR Khodaparast et al, 2018;Betti et al, 2016). APRs generally only present a danger for aggregation in situations where proteins are partially or totally unfolded, such as during protein translation or translocation, under situations of physiological stress, or due to mutations that destabilize the native conformation.…”