Bacterial Inclusion Bodies Contain Amyloid-Like Structure

Abstract

Protein aggregation is a process in which identical proteins self-associate into imperfectly ordered macroscopic entities. Such aggregates are generally classified as amorphous, lacking any long-range order, or highly ordered fibrils. Protein fibrils can be composed of native globular molecules, such as the hemoglobin molecules in sickle-cell fibrils, or can be reorganized β-sheet–rich aggregates, termed amyloid-like fibrils. Amyloid fibrils are associated with several pathological conditions in humans, including Alzheimer disease and diabetes type II. We studied the structure of bacterial inclusion bodies, which have been believed to belong to the amorphous class of aggregates. We demonstrate that all three in vivo-derived inclusion bodies studied are amyloid-like and comprised of amino-acid sequence-specific cross-β structure. These findings suggest that inclusion bodies are structured, that amyloid formation is an omnipresent process both in eukaryotes and prokaryotes, and that amino acid sequences evolve to avoid the amyloid conformation. Protein aggregation is a process by which identical proteins self-associate into imperfectly ordered macroscopic entities. Such aggregates are associated with several pathological conditions in humans, including Alzheimer disease, Parkinson disease, and diabetes type II. Furthermore, protein aggregation is a major concern in the biotechnological production of recombinant proteins and the storage of proteins, and is a central mechanism of protein folding. In general, two classes of protein aggregates are classified: first, highly ordered aggregates can be composed of native globular molecules, such as the hemoglobin molecules in sickle-cell fibrils, or reorganized into β-sheet–rich aggregates, termed amyloid-like fibrils; and second, amorphous aggregates that lack any long-range order. Here, we demonstrate that bacterial inclusion bodies, which have been believed to be made up of amorphous aggregates, are in fact amyloid-like, comprising cross-β structure that is dependent on amino-acid sequence. These findings suggest that inclusion bodies are structured, that amyloid formation is a process present in both eukaryotes and prokaryotes, that amino acid sequences can evolve to avoid the amyloid conformation, and that there might be no amorphous state of a protein aggregate.