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Abstract
Amyloids are protein fibrils with characteristic spatial structure. Though amyloids were long perceived to be pathogens that cause dozens of incurable pathologies in humans and mammals, it is currently clear that amyloids also represent a functionally important form of protein structure implicated in a variety of biological processes in organisms ranging from archaea and bacteria to fungi and animals. Despite their social significance, plants remain the most poorly studied group of organisms in the field of amyloid biology. To date, amyloid properties have only been demonstrated in vitro or in heterologous systems for a small number of plant proteins. Here, for the first time, we performed a comprehensive analysis of the distribution of potentially amyloidogenic proteins in the proteomes of approximately 70 species of land plants using the Waltz and SARP (Sequence Analysis based on the Ranking of Probabilities) bioinformatic algorithms. We analyzed more than 2.9 million protein sequences and found that potentially amyloidogenic proteins are abundant in plant proteomes. We found that such proteins are overrepresented among membrane as well as DNA- and RNA-binding proteins of plants. Moreover, seed storage and defense proteins of most plant species are rich in amyloidogenic regions. Taken together, our data demonstrate the diversity of potentially amyloidogenic proteins in plant proteomes and suggest biological processes where formation of amyloids might be functionally important.
Highlights
Amyloids represent protein fibrils consisting of monomers that form intermolecular β-sheets located along the axis of a fibril and are stabilized by numerous hydrogen bonds
We found that Gene Ontology (GO) terms enriched in proteins harboring amyloidogenic regions” (ARs) predicted by Waltz were drastically different from the terms associated with QN-rich proteins predicted by SARP
The bioinformatic analysis performed in this study revealed that potentially amyloidogenic proteins are abundant in the proteomes of land plants (Figure 1)
Summary
Amyloids represent protein fibrils consisting of monomers that form intermolecular β-sheets located along the axis of a fibril and are stabilized by numerous hydrogen bonds Such a spatial structure is called “cross-β” [1]. The term “cross-β” refers to the common pattern of amyloids in X-ray diffraction analysis with two scattering signals of approximately 4.7 and 10 Å corresponding to the distances between β-strands comprising β-sheets and between intermolecular β-sheets, respectively [2,3] Their highly ordered structure gives amyloids unusual properties including resistance to treatment with ionic detergents [4], other protein denaturants [5] and proteinases [6]. More than 30 human proteins have been shown to adopt pathological amyloid states [12]
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