Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoids.

Deena M A Gendoo,Paul M Harrison

doi:10.1371/journal.pone.0027342

Abstract

The HET-s prion-forming domain from the filamentous fungus Podospora anserina is gaining considerable interest since it yielded the first well-defined atomic structure of a functional amyloid fibril. This structure has been identified as a left-handed beta solenoid with a triangular hydrophobic core. To delineate the origins of the HET-s prion-forming protein and to discover other amyloid-forming proteins, we searched for all homologs of the HET-s protein in a database of protein domains and fungal genomes, using a combined application of HMM, psi-blast and pGenThreader techniques, and performed a comparative evolutionary analysis of the N-terminal alpha-helical domain and the C-terminal prion-forming domain of HET-s. By assessing the tandem evolution of both domains, we observed that the prion-forming domain is restricted to Sordariomycetes, with a marginal additional sequence homolog in Arthroderma otae as a likely case of horizontal transfer. This suggests innovation and rapid evolution of the solenoid fold in the Sordariomycetes clade. In contrast, the N-terminal domain evolves at a slower rate (in Sordariomycetes) and spans many diverse clades of fungi. We performed a full three-dimensional protein threading analysis on all identified HET-s homologs against the HET-s solenoid fold, and present detailed structural annotations for identified structural homologs to the prion-forming domain. An analysis of the physicochemical characteristics in our set of structural models indicates that the HET-s solenoid shape can be readily adopted in these homologs, but that they are all less optimized for fibril formation than the P. anserina HET-s sequence itself, due chiefly to the presence of fewer asparagine ladders and salt bridges. Our combined structural and evolutionary analysis suggests that the HET-s shape has “limited scope” for amyloidosis across the wider protein universe, compared to the ‘generic’ left-handed beta helix. We discuss the implications of our findings on future identification of amyloid-forming proteins sharing the solenoid fold.

Highlights

The exact atomic structure adopted by amyloid fibrils is a topic of intense debate, as high molecular weights and the polymeric character and insolubility of amyloid fibrils remain obstacles for high resolution structure determination methods such as nuclear magnetic resonance (NMR) spectroscopy [1,2,3]
Evolution of the Prion-Forming Domain Despite the inclusion of the non-redundant database (NR) database, which represents all kingdoms of life, all the identified homologs of the prion-forming domain are restricted to the fungal kingdom, and they all belong to Saccharomyceta, the Sordariomyceta (Figure 1)
In addition to Podospora anserina, these 10 homologs were from 4 other fungal species, including Nectria haematococca mpVI 17-13-4, Fusarium oxysporum, Fusarium graminearum (Gibberella zeae), and Fusarium verticilliodes (Figure 1)

Summary

Introduction

The exact atomic structure adopted by amyloid fibrils is a topic of intense debate, as high molecular weights and the polymeric character and insolubility of amyloid fibrils remain obstacles for high resolution structure determination methods such as nuclear magnetic resonance (NMR) spectroscopy [1,2,3]. While atomicresolution structures of the infectious fibrils for many prions and amyloid-forming proteins are still lacking, recent studies have presented the first well-defined atomic structure of a functional amyloid, based on amyloid fibrils of the HET-s yeast prion [6,7]. The HET-s prion forming domain (PFD) is necessary and sufficient for amyloid formation in vitro, as well as prion propagation in vivo [8,11,12]. Fibrils formed from this PFD are described as a left-handed b-solenoid composed of four parallel, stacked pseudo-repeated b-helices; the pseudo-repeats are a result of one molecule forming two turns of the solenoid [6,7]. In addition to intra- and intermolecular hydrogen bonds between the pseudo-repeats, the solenoid structure is stabilized by favourable side-chain contacts, such as salt bridges, between oppositely charged residues facing outside of the triangular core [6,7]

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Results

Conclusion