Biology subjects

Sanchez de Groot, N.

Publications and source records attributed to Sanchez de Groot, N..

10 recordsLinked to original sources

bioRxiv2026

Sequential Molecular Interactions Shape Aβ42 Aggregation, Propagation, and Toxicity

Protein aggregation is a context-dependent process in which the molecular environment can influence the properties of the resulting assemblies. In biological systems, these interactions can occur sequentially, as aggregates formed in one cellular or tissue context may encounter different molecular partners and act as seeds in subsequent aggregation events. Here, we used sequential seeding as a controlled experimental model of this temporal and contextual complexity to investigate how prion-like sequences from the gut microbiome modulate amyloid-{beta} aggregation across successive aggregation cycles. Combining kinetic, biophysical, conformational, and toxicity analyses, we show that early interactions with exogenous peptides modify the properties of first-generation A{beta}40- and A{beta}42-derived seeds, resulting in propagated A{beta}42 assemblies with distinct molecular and functional properties. These findings support an Interaction History model in which exogenous sequences bias the emergence of aggregate populations whose properties and subsequent propagation depend on the molecular contexts experienced during earlier aggregation events. Overall, our results present A{beta} aggregation as a history-dependent process and suggest that single-step assays may fail to capture aggregate diversity that emerges across successive aggregation cycles.

biochemistry↗

bioRxiv2025

Exogenous Amyloid Sequences: Their Role in Amyloid-Beta Heterotypic Aggregation

Protein aggregation is a complex process influenced by environmental conditions and interactions between multiple molecules, including those of exogenous origin. Although in vitro simulations of aggregation are crucial for advancing research, few studies explore cross-seeding as a repeating event, despite the potential for such events when proteins circulate through the body. Here, we investigated the impact of exogenous amyloid sequences derived from the gut microbiota on the heterotypic aggregation of A{beta} peptides. We utilized ten 21-amino acid peptides derived from bacterial genomes, previously shown to interfere with A{beta}40 aggregation and induce memory loss in Caenorhabditis elegans. Through consecutive cross-seeding assays with A{beta}40 and A{beta}42, we analyzed the effects of these peptides on aggregation kinetics and seed propagation. Our findings indicate that exogenous molecules can influence A{beta}s aggregation process, altering the fibrils properties. Based on this, we introduce the "Interaction History" concept, where prior interactions shape the aggregation and propagation of A{beta} peptides. This work supports the idea that environmental factors, such as microbial amyloids, can contribute to the heterogeneity and progression of amyloid-related diseases. Our results highlight the need for therapeutic strategies targeting diverse amyloid configurations and reinforce the importance of considering exogenous sequences as additional triggers in AD pathology.

biochemistry↗

bioRxiv2023

Microbiome-Derived Prion-Like Proteins and Their Potential to Trigger Cognitive Dysfunction

Our life is intricately connected to microorganisms through infection or symbiotic relationships. While the inter-species propagation of prion-like proteins is well-established, their presence in the microbiome and impact on the host remains largely unexplored. To address this, we conducted a systematic study integrating in silico, in vitro, and in vivo analyses, showing that 63% of the gastrointestinal tract microbiome encodes prion-like sequences. These sequences can form amyloid fibrils capable of interfering with the aggregation of the Amyloid-beta-peptide and promoting the aggregation and propagation of the Sup35 prion. Finally, when C. elegans were fed with bacteria expressing chimeras of our prion candidates, it resulted in the loss of sensory memory, reproducing the Alzheimers model phenotype. In our model, memory impairment is linked to aggregate fragmentation and its susceptibility to degradation. Taken together, these findings show that the gut microbiota serves as a potential reservoir of prion-like sequences, supporting the idea that microbial products may influence the pathogenesis of neurodegenerative diseases.

molecular biology↗

bioRxiv2022

The PRALINE database: Protein and Rna humAn singLe nucleotIde variaNts in condEnsates

SummaryBiological condensates are membraneless organelles with different material properties. Proteins and RNAs are the main components, but most of their interactions are still unknown. Here we introduce PRALINE, a database for the interrogation of proteins and RNAs contained in stress-granules, processing bodies, and other assemblies including droplets and amyloids. PRALINE provides information about the predicted and experimentally validated protein-protein, protein-RNA and RNA-RNA interactions. For proteins, it reports the liquid-liquid phase separation and liquid-solid phase separation propensities. For RNAs, it provides information on predicted secondary structure content. PRALINE shows detailed information on human single-nucleotide variants, their clinical significance and presence in protein and RNA binding sites, and how they can affect condensates physical properties. AvailabilityPRALINE is freely accessible on the web at http://alvinlee.bio.uniroma1.it/praline. Supplementary informationGeneral information is at http://alvinlee.bio.uniroma1.it/praline/about, where we provide a detailed description of the datasets and the tools employed in the database. Data provided in PRALINE are available at http://alvinlee.bio.uniroma1.it/praline/downloads. The tutorial is at http://alvinlee.bio.uniroma1.it/praline/tutorial.

bioinformatics↗

bioRxiv2022

A high-throughput approach to predict A-to-I effects on RNA structure indicates a change of double-stranded content in non-coding RNAs

RNA molecules undergo a number of chemical modifications whose effects can alter their structure and molecular interactions. Previous studies have shown that RNA editing can impact the formation of ribonucleoprotein complexes and influence the assembly of membrane-less organelles such as stress-granules. For instance, N6-methyladenosine (m6A) enhances SG formation and N1-methyladenosine (m1A) prevents their transition to solid-like aggregates. Yet, very little is known about adenosine to inosine (A-to-I) modification that is very abundant in human cells and not only impacts mRNAs but also non-coding RNAs. Here, we built the CROSSalive predictor of A-to-I effects on RNA structure based on high-throughput in-cell experiments. Our method shows an accuracy of 90% in predicting the single and double-stranded content of transcripts and identifies a general enrichment of double-stranded regions caused by A-to-I in long intergenic non-coding RNAs (lincRNAs). For the individual cases of NEAT1, NORAD and XIST, we investigated the relationship between A-to-I editing and interactions with RNA-binding proteins using available CLIP data. We found that A-to-I editing is linked to alteration of interaction sites with proteins involved in phase-separation, which suggests that RNP assembly can be influenced by A-to-I. CROSSalive is available at http://service.tartaglialab.com/new_submission/crossalive.

biochemistry↗

bioRxiv2021

A spoonful of disorder regulates interactions within Stress Granules and Processing Bodies

Condensation, or liquid-like phase separation, is a phenomenon indispensable for the spatiotemporal regulation of molecules within the cell. Recent studies indicate that the composition and molecular organization of phase-separated organelles such as Stress Granules (SGs) and Processing Bodies (PBs) are highly variable and dynamic. A dense contact network involving both RNAs and proteins controls the formation of SGs and PBs and an intricate molecular architecture, at present poorly understood, guarantees that these assemblies sense and adapt to different stresses and environmental changes. Here, we investigated the physico-chemical properties of SGs and PBs components and studied the architecture of their interaction networks. We found that proteins and RNAs establishing the largest amount of contacts in SGs and PBs have distinct structural properties and intrinsic disorder is enriched in all protein-RNA, protein-protein and RNA-RNA interaction networks. The increase of disorder in proteins is accompanied by an enrichment in single-stranded regions of RNA binding partners. Our results suggest that SGs and PBs quickly assemble and disassemble through fuzzy-like dynamic contacts modulated by unfolded domains of their components. Research HighlightsO_LIWe systematically studied RNA-RNA, protein-protein and RNA-protein interaction networks in stress granules and processing bodies; C_LIO_LIRNAs enriched in stress granules and processing bodies are more single-stranded and form a large number of contacts with both proteins and RNAs; C_LIO_LIProteins in stress granules and processing bodies are less structured and contact larger amounts of single-stranded RNAs. C_LI

molecular biology↗

bioRxiv2020

Bacteria Use Structural Imperfect Mimicry To Hijack The Host Interactome

Bacteria use protein-protein interactions to infect their hosts and hijack fundamental pathways, which ensures their survival and proliferation. Hence, the infectious capacity of the pathogen is closely related to its ability to interact with host proteins. Here, we show that hubs in the host-pathogen interactome are isolated in the pathogen network by adapting the geometry of the interacting interfaces. An imperfect mimicry of the eukaryotic interfaces allows pathogen proteins to actively bind to the hosts target while preventing deleterious effects on the pathogen interactome. Understanding how bacteria recognize eukaryotic proteins may pave the way for the rational design of new antibiotic molecules.

microbiology↗

bioRxiv2020

RNA-Binding and Prion Domains: The Yin and Yang of Phase Separation

Biomolecular condensates are membrane-less organelles mainly composed of proteins and RNAs that organize intracellular spaces and regulate biochemical reactions. The ability of proteins and RNAs to phase separate is encoded in their sequences, yet it is still unknown which domains drive the process and what are their specific roles. Here, we systematically investigated the human and yeast proteomes to find regions promoting biomolecular condensation. Using advanced computational models to predict the phase separation propensity of proteins, we designed a set of experiments to investigate the contributions of Prion-Like Domains (PrLDs) and RNA-Binding Domains (RBDs). We found that while just one PrLD is sufficient to drive protein condensation, multiple RBDs are needed to modulate the dynamicity of the assemblies. In the case of stress granule protein Pub1 we show that the PrLD promotes sequestration of protein partners and the RBD confers liquid-like behaviour to the condensate. Our work sheds light on the fine interplay between RBDs and PrLD to regulate formation of membrane-less organelles, opening up the avenue for their manipulation.

molecular biology↗

bioRxiv2019

The fitness cost and benefit of phase separated protein deposits

Phase separation of soluble proteins into insoluble deposits is associated with numerous diseases. However, protein deposits can also function as membrane-less compartments for many cellular processes. What are the fitness costs and benefits of forming such deposits in different conditions? Using a model protein that phase separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast. The environmental condition and the cellular demand for the protein function emerge as key determinants of fitness. Protein deposit formation can lead to cell-to-cell differences in free protein abundance between individuals. This results in variable manifestation of protein function and a continuous range of phenotypes in a cell population, favoring survival of some individuals in certain environments. Thus, protein deposit formation by phase separation might be a mechanism to sense protein concentration in cells and to generate phenotypic variability. The selectable phenotypic variability, previously described for prions, could be a general property of proteins that can form phase separated assemblies and may influence cell fitness.\n\nStand-first textUsing a model protein that phase separates into deposits, we distinguish and quantify the fitness contribution due to the loss or gain of protein function and deposit formation in yeast.\n\nO_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY\n\nBullet pointsO_LIThe presented approach identifies and quantifies different fitness effects associated with protein deposit formation due to phase separation\nC_LIO_LIThe environmental condition and the cellular demand for the protein function emerge as key determinants of fitness upon protein deposit formation\nC_LIO_LIVariability in protein deposit formation can lead to cell-to-cell differences in free protein abundance between individuals\nC_LIO_LIProtein phase separation can generate a continuous range of phenotypes in a cell population\nC_LI

systems biology↗

bioRxiv2018

Insights into the structure-driven protein interactivity of RNA molecules

The combination of high-throughput sequencing and in vivo crosslinking approaches leads to the progressive uncovering of the complex interdependence between cellular transcriptome and proteome. Yet the molecular determinants that govern interactions in protein-RNA networks are poorly known at present. Here we used the most recent experimental data to investigate the relationship between RNA structure and protein interactions. Our results show that, independently of the particular technique, the amount of structure in RNA molecules correlates with the capacity of binding to proteins in vitro and in vivo. To validate this observation, we generated an in vitro network that mimics the composition of phase-separated RNA granules. We observed that RNA, when structured, competes with protein binding and can rearrange the interaction network. The simplicity of the principle bears great potential to boost the understanding and modelling of cellular processes involving RNA-protein interactions.

molecular biology↗