Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties

Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here, we use quantitative proteomics in the African turquoise killifish to identify protein aggr...

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Published inCell reports (Cambridge) Vol. 43; no. 6; p. 112787
Main Authors Harel, Itamar, Chen, Yiwen R., Ziv, Inbal, Singh, Param Priya, Heinzer, Daniel, Navarro Negredo, Paloma, Goshtchevsky, Uri, Wang, Wei, Astre, Gwendoline, Moses, Eitan, McKay, Andrew, Machado, Ben E., Hebestreit, Katja, Yin, Sifei, Sánchez Alvarado, Alejandro, Jarosz, Daniel F., Brunet, Anne
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 25.06.2024
Subjects
aggregates
aging
killifish
N. furzeri
phase separation
N. furzeri
phase separation
CP: Cell biology
CP: Neuroscience
killifish
aggregates
aging
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Summary:Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here, we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA-binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms aggregate-like puncta in the brains of old killifish and mice. Interestingly, DDX5’s prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the protein’s ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline. [Display omitted] •Quantitative identification of proteins that aggregate in old killifish brains•The RNA helicase DDX5 forms aggregate-like puncta in old vertebrate brains•DDX5 aggregates exhibit prion-like behavior and seed the formation of new aggregates•DDX5 forms condensates that enhance its activity but mature into inactive aggregates Harel, Chen, and colleagues describe the systematic identification of proteins that aggregate in old vertebrate brains. Interestingly, one of these proteins, the RNA helicase DDX5, seeds the formation of new aggregates in a “prion-like” behavior. These findings could have implications for the age dependency of cognitive decline.
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Present address: Bakar Aging Research Institute, University of California, San Francisco, San Francisco, CA 94143, USA
Present address: National Institute of Biological Sciences, Beijing 102206, China
These authors contributed equally
Senior author
Present address: Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
AUTHOR CONTRIBUTIONS
Lead contact
I.H., Y.R.C., I.Z., A.B., and D.F.J. designed mass spectrometry experiments. I.H. isolated killifish organs, and Y.R.C. and I.Z. isolated samples for mass spectrometry with the help of I.H. and performed silver stain analysis. Y.R.C. designed and implemented mass spectrometry data analysis and performed domain enrichment analyses with input from I.H., P.P.S., A.B., and D.F.J. I.H. generated mammalian constructs, performed and analyzed killifish immunocytochemistry experiments and some 293T experiments, and generated DDX5 CRISPR knockout and and DDX5 antibody. Y.R.C. generated yeast constructs with help from I.H. and B.E.M. and performed and analyzed yeast aggregation and FRAP experiments. Y.R.C. generated and purified recombinant killifish DDX5 proteins and performed and analyzed phase-separation and activity assays. P.P.S. conducted PCA and GO term analyses. D.H. performed and analyzed 293T experiments and assembled the revised version of the manuscript. P.N.N. performed and analyzed DDX5 immunocytochemistry experiments in mice. U.G. and G.A. performed and analyzed immunocytochemistry experiments in killifish and western blot for DDX5, respectively, under the supervision of I.H. I.H. generated the transgenic DDX5 construct, and W.W. generated the transgenic killifish overexpressing DDX5 under the supervision of A.S.A. E.M. and A.M. provided young and old killifish brain sections. K.H. performed initial analysis of mass spectrometry data. S.Y. helped with sequence verification and cloning of killifish constructs. I.H., Y.R.C., D.F.J., and A.B. wrote the paper, and all authors commented on the manuscript.
ISSN:2211-1247
2211-1247
DOI:10.1016/j.celrep.2023.112787