Toxicity in amyloid diseases is intimately linked to the nature of aggregates, with early oligomeric species believed to be more cytotoxic than later fibrillar aggregates. Yet mechanistic understanding of how aggregating species evolve with time is currently lacking. We have explored the aggregation process of a chimera composed of a globular protein (cellular retinoic acidbinding protein, CRABP) and huntingtin exon 1 with polyglutamine tracts either above (Q53) or below (Q20) the pathological threshold using Escherichia coli cells as a model intracellular environment. Previously we showed that fusion of the huntingtin exon 1 sequence with >40Q led to structural perturbation and decreased stability of CRABP (Ignatova, Z., and Gierasch, L. M. (2006) J. Biol. Chem. 281, 12959 -12967). Here we report that the Q53 chimera aggregates in cells via a multistep process: early stage aggregates are spherical and detergent-soluble, characteristics of prefibrillar aggregates, and appear to be dominated structurally by CRABP, in that they can promote aggregation of a CRABP variant but not oligoglutamine aggregation, and the CRABP domain is relatively sequestered based on its protection from proteolysis. Late stage aggregates appear to be dominated by polyGln; they are fibrillar, detergent-resistant, capable of seeding aggregation of oligoglutamine but not the CRABP variant, and show relative protection of the polyglutamine-exon1 domain from proteolysis. These results point to an evolution of the dominant sequences in intracellular aggregates and may provide molecular insight into origins of toxic prefibrillar aggregates.Protein aggregation is associated with an expanding set of diseases, yet a clear correlation between the mechanism of aggregation and pathology is generally lacking. In the specific example of the polyglutamine (polyQ) 3 disease family, to which Huntington disease belongs, pathology is almost invariably associated with mutations that increase the number of glutamine residues in the corresponding protein over a pathological threshold value of 30 -40 repeats (1). But the direct role of polyQ extensions in toxicity has been questioned due to the poor correlation between the presence of visible aggregates and pathological symptoms in post-mortem studies and cell culture models (2-4). Complicating efforts to understand how aggregation correlates with pathology in glutamine repeat diseases is the compelling evidence from several systems that the nature of aggregates formed by polyQ-containing proteins evolves over time. In vitro studies showed that the fibrillization of expressed huntingtin (Htt) exon 1 containing a long polyQ stretch is a multistep process with early formation of globular oligomers (5-7), similar to the metastable oligomers and protofibrils identified in the aggregation of both Alzheimer amyloid plaque peptide A (8, 9) and ␣-synuclein (10, 11). Of crucial importance to understanding the impact of the multistage aggregation events is the growing evidence, albeit largely from cell culture, that the...