Mutation-induced filaments of folded proteins are inert and non-toxic in a cellular system

Filamentous protein assemblies are essential for cellular functions but can also form aberrantly through mutations that induce self-interactions between folded protein subunits. These assemblies, which we refer to as agglomerates, differ from aggregates and amyloids that arise from protein misfolding. While cells have quality control mechanisms to identify, buffer, and eliminate aggregates, it is unknown whether similar mechanisms exist for agglomerates. Here, we define and characterize this distinct class of assemblies formed by the polymerization of folded proteins. To systematically assess their cellular impact, we developed a simple in-cell assay that distinguishes agglomerates from aggregates based on co-assembly with wild-type subunits. Unlike misfolded aggregates, we show that agglomerates retain their folded state, do not colocalize with the proteostasis machinery, and are not ubiquitinated. Moreover, agglomerates cause no detectable growth defects. Quantitative proteomics also revealed minor changes in protein abundance in cells expressing agglomerates. These results position agglomerates as a structurally and functionally distinct class of protein assemblies that are largely inert in cells, highlighting their potential as building blocks for intracellular engineering and synthetic biology.