Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease

Abstract

Positively charged repeat peptides are emerging as key players in neurodegenerative diseases. These peptides can perturb diverse cellular pathways but a unifying framework for how such promiscuous toxicity arises has remained elusive. We used mass-spectrometry-based proteomics to define the protein targets of these neurotoxic peptides and found that they all share similar sequence features that drive their aberrant condensation with these positively charged peptides. We trained a machine learning algorithm to detect such sequence features and unexpectedly discovered that this mode of toxicity is not limited to human repeat expansion disorders but has evolved countless times across the tree of life in the form of cationic antimicrobial and venom peptides. We demonstrate that an excess in positive charge is necessary and sufficient for this killer activity, which we name polycation poisoning. These findings reveal an ancient and conserved mechanism and inform ways to leverage its design rules for new generations of bioactive peptides.

Sequence-ensemble-function relationships for disordered proteins in live cells

“…Based on these independent observations, we speculate that IDRs with a strong net positive charge unavoidably recruit polyanions, leading to ensemble compaction driven by intermolecular charge neutralization (complex coacervation). This interpretation is at least consistent with the “polycation poisoning” model proposed by Boeynaems et al 46 .…”

“…Indeed, biomacromolecules (including phospholipids, nucleic acids, and even the human proteome) tend to be negatively charged 44,45 . Recent proteome-wide analysis across various species coupled with extant quantitative mass spectrometry found very few cases of highly abundant IDRs with a strong net positive charge 46 . The few IDRs that did contain a strong positive charge were expected to be constitutively bound to nucleic acids, anchored in phospholipid bilayers, or at least partially neutralized via phosphorylation.…”

Charge-Patterned Disordered Peptides Tune Intracellular Phase Separation in Bacteria

“…This is in line with recent reports of the cellular toxicity of cationic peptides and proteins. 45,46 Interestingly, the peptide sequences studied here also bear a close resemblance with antimicrobial peptides, which are typically cationic and 10−25 amino acidlong. Such peptides have been shown to inhibit transcription and translation in vitro and form condensate-like clusters with nucleic acids in bacteria.…”

“…When the use of these cationic peptides for applications in synthetic biology is designed, it is important to note that the peptides can have some modest impacts on cell growth (Figure S2A). This is in line with recent reports of the cellular toxicity of cationic peptides and proteins. , Interestingly, the peptide sequences studied here also bear a close resemblance with antimicrobial peptides, which are typically cationic and 10−25 amino acid-long. Such peptides have been shown to inhibit transcription and translation in vitro and form condensate-like clusters with nucleic acids in bacteria …”

C9orf72-linked arginine-rich dipeptide repeats aggravate pathological phase separation of G3BP1

“…As a final note, we should not miss that besides ALS/FTD, RAN translation generates potentially aggregation-prone peptide repeats in at least 10 repeat expansion disorders [49] Poly-GP and poly-PR feature in spinocerebellar ataxia 36 (SCA36) [50], poly-EG and and poly-RE in X-linked dystonia parkinsonism (XDP) [51], and poly-LPAC and poly-QAGR in myotonic dystrophy type 2 (DM2) [52]. In addition, repetitive, cationic peptides are used by a broad range of organisms as venoms, toxins and antimicrobials [53,54], which may similarly target a broad range of host RBPs involved in biomolecular condensation as their primary modality of toxicity. In accord, the mechanistic insight generated here may not only open novel avenues for targeting ALS/FTD, but it may also help better understand these related biological phenomena at the molecular level.…”