Predicting Amyloidogenic Proteins in the Proteomes of Plants

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.

Accumulation of storage proteins in plant seeds is mediated by amyloid formation

“…Previously, we performed a large-scale bioinformatic analysis of potentially amyloidogenic properties of plant proteins including all annotated proteomes of land plant species [22]. This screening demonstrated that seed storage proteins comprising the evolutionary conservative β-barrel domain Cupin-1 were rich in amyloidogenic regions in the majority of analyzed species [22].…”

Plant Prionome maps reveal specific roles of prion-like proteins in stress and memory

“…Another interesting category of proteins in the plant prionomes is that of Ts/RTRs, which constitutes 3.4% of the total PrLPs identified from all species. Though prionomes of several organisms have been predicted including those of plants (Antonets and Nizhnikov, 2017) but Ts/RTRs found no mention in any of the previous studies, despite the rice prionome constituting a huge 65% share. Presence of RTRs/Tstype of PrLPs in plants is intriguing, but indications about their prion-like roles have been reported in human and animal brains, where transposon activity plays a potentially important role in the pathogenesis of prion diseases (Mustafin and Khusnutdinova, 2018).…”

Universal and taxon-specific trends in protein sequences as a function of age

“…We speculate that plants are simply better at coping with proteostasis than other taxonomic groups, using mechanisms other than high ISD to protect themselves from protein misfolding and aggregation. Plant proteomes are rich in predicted amyloidogenic regions (Antonets & Nizhnikov 2017a), and yet there is a paucity of evidence for aggregate formation in plants under normal conditions (Antonets & Nizhnikov 2017b). This is perhaps due in part to the presence of molecules such as polyphenols, which inhibit aggregation (Velander et al 2017).…”