Functional amyloids in the microbiomes of a rat Parkinson's disease model and wild-type rats

Cross-seeding between amyloidogenic proteins in the gut is receiving increasing attention as a possible mechanism for initiation or acceleration of amyloid formation by aggregation-prone proteins such as SN, which is central in the development of Parkinsons disease. This is particularly pertinent in view of the growing number of functional (i.e. benign and useful) amyloid proteins discovered in bacteria. Here we identify two functional amyloid proteins, Pr12 and Pr17, in fecal matter from Parkinsons disease transgenic rats and their wild type counterparts, based on their stability against dissolution by formic acid. Both proteins show robust aggregation into ThT-positive aggregates that contain higher-order {beta}-sheets and have a fibrillar morphology, indicative of amyloid proteins. In addition, Pr17 aggregates formed in vitro showed significant resistance against formic acid, suggesting an ability to form highly stable amyloid. Treatment with proteinase K revealed a protected core of approx. 9 kDa. Neither Pr12 nor Pr17, however, affected SN aggregation in vitro. Thus, amyloidogenicity does not per se lead to an ability to cross-seed fibrillation of SN. Our results support the use of proteomics and formic acid to identify amyloid protein in complex mixtures and indicates the existence of numerous functional amyloid proteins in microbiomes. IMPORTANCEThe bacterial microbiome in the gastrointestinal tract is increasingly seen as important for human health and disease. One area of particular interest is that of neurodegenerative diseases such as Parkinsons which involve pathological aggregation into amyloid of human proteins such as - synuclein (SN). Bacteria are known to form benign or functional amyloid, some of which may initiate unwanted aggregation of e.g. SN in the enteric nervous system through cross-seeding via contact with the microbiome. Here we show that the rat microbiome contains several proteins which form this type of amyloid aggregate both in vivo and in vitro. Although the two proteins we investigate in depth do not directly promote SN aggregation, our work shows that the microbiome potentially harbors a significant number of bacterial amyloid which could play a role in human physiology at various levels.