The prion-like RNA-processing protein HNRPDL forms inherently toxic amyloid-like inclusion bodies in bacteria

Abstract

BackgroundThe formation of protein inclusions is connected to the onset of many human diseases. Human RNA binding proteins containing intrinsically disordered regions with an amino acid composition resembling those of yeast prion domains, like TDP-43 or FUS, are being found to aggregate in different neurodegenerative disorders. The structure of the intracellular inclusions formed by these proteins is still unclear and whether these deposits have an amyloid nature or not is a matter of debate. Recently, the aggregation of TDP-43 has been modelled in bacteria, showing that TDP-43 inclusion bodies (IBs) are amorphous but intrinsically neurotoxic. This observation raises the question of whether it is indeed the lack of an ordered structure in these human prion-like protein aggregates the underlying cause of their toxicity in different pathological states.ResultsHere we characterize the IBs formed by the human prion-like RNA-processing protein HNRPDL. HNRPDL is linked to the development of limb-girdle muscular dystrophy 1G and shares domain architecture with TDP-43. We show that HNRPDL IBs display characteristic amyloid hallmarks, since these aggregates bind to amyloid dyes in vitro and inside the cell, they are enriched in intermolecular β-sheet conformation and contain inner amyloid-like fibrillar structure. In addition, despite their ordered structure, HNRPDL IBs are highly neurotoxic.ConclusionsOur results suggest that at least some of the disorders caused by the aggregation of human prion-like proteins would rely on the formation of classical amyloid assemblies rather than being caused by amorphous aggregates. They also illustrate the power of microbial cell factories to model amyloid aggregation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-015-0284-7) contains supplementary material, which is available to authorized users.

The Rho Termination Factor of Clostridium botulinum Contains a Prion-Like Domain with a Highly Amyloidogenic Core

“…Thus RNA binding is required to activate the RNA-dependent ATPase activity of Rho. The predicted PrD and the RNA binding domain are contiguous in Rho, a topology that is also found in many eukaryotic prion-like proteins ( King et al, 2012 ; Espinosa Angarica et al, 2013 ; Malinovska et al, 2013 ; Navarro et al, 2015 ).…”

hnRNPDL Phase Separation Is Regulated by Alternative Splicing and Disease-Causing Mutations Accelerate Its Aggregation

“…Mutation of Asp378 of hnRNPDL to either Asn or His has been associated with LGMD1G (Berardo et al, 2019;Sun et al, 2019;Vieira et al, 2014). As in the case of hnRNPA1 and hnRNPA2, this Asp maps at the PrLD of hnRNPDL (Figure 6A; Navarro et al, 2015) and it is strictly conserved in vertebrates (Figure S7). Therefore, we examined how these mutations affect LLPS and the aggregation of hnRNPDL protein.…”

“…Interestingly, hnRNPDL D378N/H point mutations reside in the PrLD of hnRNPDL (Navarro et al, 2015). Disease-causing mutations in PrLDs have been discovered in other prion-like proteins, for example in hnRNPA1 and hnRNPA2 proteins (Kim et al, 2013), in both cases involving the replacement of a single Asp residue, as in hnRNPDL.…”

Emergence and evolution of yeast prion and prion-like proteins

“…Mutations in two yeast-prion-like proteins hnRNPA2B1 and hnRNPA1 initiate neurodegenerative disease in humans through amyloid formation [ 37 ]. HNRPDL has a yeast-prion-like domain, and has been linked to development of limb-girdle muscular dystrophy 1G [ 38 ]. Also, pathogenic proteins in at least nine other neurodegenerative disorders have disease-linked poly-Q expansions.…”