Abstract
Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its “prionome.” In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.
Highlights
Plant memory has emerged as one of the most fascinating fields of study in modern science, especially in view of the intricate mechanisms evolved by plants to survive under everchanging unfavorable and adverse environmental conditions
In terms of absolute numbers, we identified 4,479 Prion-like proteins (PrLPs), which were classified into 10 functional categories (Figure 1B)
Amyloidogenic PrLPs in moss genomes may have contributed to biofilm formation as the determinants of high mechanical resistance of exopolysaccharides (Mostaert et al, 2009), seen in bacteria (Romero et al, 2010). This was followed by a detailed Gene ontology (GO) enrichment analysis of all plant prionomes that offered insights into functional diversity, we found chlorophyte PrLPs to be enriched in signaling-related genes especially, mitogen-activated protein kinase (MAPK), protein kinases, and response regulators
Summary
Plant memory has emerged as one of the most fascinating fields of study in modern science, especially in view of the intricate mechanisms evolved by plants to survive under everchanging unfavorable and adverse environmental conditions. Prions caught the attention of the scientific world through Pruisiner’s pioneering work two decades ago (Prusiner, 1998) These proteins can switch from nonaggregated states to self-templating highly ordered aggregates and transmit the same to other homologous polypeptide sequences. Prion form of the protein can act as a bet-hedging device to offer a growth advantage under stressful environments, such as Sup protein from yeast, the prion form [PSI+] of which is positively selected under stressful conditions in exchange for a reduced overall fitness (Newby and Lindquist, 2013; Franzmann et al, 2018) In humans, diseases such as Alzheimer’s, Parkinson’s, amyotrophic lateral sclerosis, and Huntington’s syndrome are associated with amyloid proteins, which have certain prion-like properties but unlike typical prion diseases they are not transmissible (Schwab et al, 2008; Nonaka et al, 2013; Iglesias et al, 2019)
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