In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases

Iglesias, Valentín; Paladin, Lisanna; Juan-Blanco, Teresa; Pallarès, Irantzu; Aloy, Patrick; Tosatto, Silvio C. E.; Ventura, Salvador

doi:10.3389/fphys.2019.00314

Cited by 22 publications

(23 citation statements)

References 95 publications

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“…In algae, these amyloidogenic prion-like proteins may enable bio lm formation as determinants of high mechanical resistance of exo-polysaccharides [35], also seen in bacteria [36], supported further by the fact that we found all four chlorophytes in this study, enriched in signalling-related genes especially, mitogen-activated protein kinases (MAPK), protein kinases, and response regulators. A consensus on overrepresentation of nucleic acid binding functions among the amyloid-forming proteins exists already, and is a common characteristic of PrLPs (Silva and Cordeiro, 2016;Iglesias et al, 2019), and this too, is further corroborated by our results that indicate 40% of PrLPs to have RNA and DNA binding functions in the plant prionomes.…”

Section: Discussionsupporting

confidence: 86%

Prion-like proteins reveal crosstalk between Stress and Memory pathways in Plants

Garai¹,

Citu²,

Singla-Pareek³

et al. 2021

Preprint

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Background: Prions can be 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. Results: In this work, we report the widespread presence of PrLPs in plants through a comprehensive analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species, and we term the entire PrLP complement of a genome, as it’s Prionome . Investigation of rice transcriptomic datasets further delineated the role of PrLPs in stress and developmental responses, leading us to explore whether and to what extent PrLPs may build stress memory. We found the rice prionome to be significantly enriched for Transposons/Retrotransposons (Ts/RTRs), and superimposed it with the corresponding interactome and diurnal transcriptome. Regulatory inferences derived from clustering and overlaying of these datasets revealed a complex network and crosstalk between PrLPs, transcription factors and genes known to be involved in stress priming. Conclusion: This work connects transient and trans-generational memory mechanisms in plants with prion-like proteins, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. We derive transcriptional regulatory inferences from the rice diurnal gene expression data to identify specific prion-like genes that may be memory hubs in rice. Taken together, our work provides important insights into the anticipated role of prions in stress and memory, paving the way for more focussed studies for validating role of identified PrLPs in memory acclimation.

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Section: Discussionsupporting

confidence: 86%

Prion-like proteins reveal crosstalk between Stress and Memory pathways in Plants

Garai¹,

Citu²,

Singla-Pareek³

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…In algae, these amyloidogenic prion-like proteins may enable biofilm formation as determinants of high mechanical resistance of exo-polysaccharides (Mostaert et al, 2009), also seen in bacteria (Romero et al, 2010), supported further by the fact that we found all four chlorophytes in this study, enriched in signallingrelated genes especially, mitogen-activated protein kinases (MAPK), protein kinases, and response regulators. A consensus on overrepresentation of nucleic acid binding functions among the amyloid-forming proteins exists already, and is a common characteristic of PrLPs (Silva and Cordeiro, 2016;Iglesias et al, 2019), and this too, is further corroborated by our results that indicate 40% of PrLPs to have RNA and DNA binding functions in the plant prionomes.…”

Section: Discussionsupporting

confidence: 86%

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

Garai

Citu

Pandey

et al. 2020

Preprint

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Prions can be considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been demonstrated to be present in plants, but their role in plant stress and memory remains largely unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with plant prionomes. Investigation of the rice transcriptome further delineated the role of PrLPs in stress and developmental responses, leading us to explore whether and to what extent PrLPs may build stress memory. The rice prionome is significantly enriched for Transposons/Retrotransposons (Ts/RTRs), and we derived transcriptional regulatory inferences from diurnal gene expression revealing a complex regulatory network between PrLPs, transcription factors and genes known to be involved in stress priming, as well as transient and trans-generational plant memory. Overall, our data suggest that plant memory mechanisms may rely upon protein-based signals embedded in PrLPs, in addition to chromatin-based epigenetic signals and provides important insights into the anticipated role of prions in stress and memory.

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“…A significant fraction of proteins involved in transcriptional regulation both in yeast and mammalian cells contain sequences, enriched by Q and/or N residues that are similar to prion domains (PrDs) of yeast prions [ 31 , 32 , 33 ] and therefore termed PrD-like domains (PrDL). However, the abilities of the majority of these proteins to form an amyloid and their potential role as amyloids are not studied.…”

Section: Introductionmentioning

confidence: 99%

Functional Mammalian Amyloids and Amyloid-Like Proteins

Rubel

Fedotov

Grizel

et al. 2020

Life

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Amyloids are highly ordered fibrous cross-β protein aggregates that are notorious primarily because of association with a variety of incurable human and animal diseases (termed amyloidoses), including Alzheimer’s disease (AD), Parkinson’s disease (PD), type 2 diabetes (T2D), and prion diseases. Some amyloid-associated diseases, in particular T2D and AD, are widespread and affect hundreds of millions of people all over the world. However, recently it has become evident that many amyloids, termed “functional amyloids,” are involved in various activities that are beneficial to organisms. Functional amyloids were discovered in diverse taxa, ranging from bacteria to mammals. These amyloids are involved in vital biological functions such as long-term memory, storage of peptide hormones and scaffolding melanin polymerization in animals, substrate attachment, and biofilm formation in bacteria and fungi, etc. Thus, amyloids undoubtedly are playing important roles in biological and pathological processes. This review is focused on functional amyloids in mammals and summarizes approaches used for identifying new potentially amyloidogenic proteins and domains.

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In silico Characterization of Human Prion-Like Proteins: Beyond Neurological Diseases

Cited by 22 publications

References 95 publications

Prion-like proteins reveal crosstalk between Stress and Memory pathways in Plants

Prion-like proteins reveal crosstalk between Stress and Memory pathways in Plants

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

Functional Mammalian Amyloids and Amyloid-Like Proteins

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