Biology subjects

Jarosz, D. F.

Publications and source records attributed to Jarosz, D. F..

18 recordsLinked to original sources

bioRxiv2026

Prion-induced heritable states in Caenorhabditis elegans

Self-replicating protein conformations can encode persistent epigenetic states that underlie prion diseases and contribute to age-related neurodegenerative disorders in mammals. In fungi, such conformers are transmitted through mitosis and meiosis, enabling robust inheritance of diverse phenotypes. Whether analogous transgenerational protein-based inheritance extends beyond unicellular systems to metazoans remains unknown. Here, we address this question in C. elegans, a genetically tractable, short-lived animal well suited for tracking the transmission of heritable information across generations. We found that a yeast prion domain, when fused to a host protein, induced a heritable altered state that arose at elevated temperatures and persisted across generations at lower temperatures. The emergence of this state depended on known prionogenic yeast repeats, while the state itself was reversible and behaved semi-dominantly in crosses, consistent with a protein-based epigenetic mechanism. These findings provide direct evidence that protein domains capable of adopting self-replicating conformers can encode heritable information in an animal.

genetics↗

bioRxiv2026

eSIG-Net: Accurate prediction of single-mutation induced perturbations on protein interactions using a language model

Most proteins exert their functions in complex with other interactors. Single mutations can exhibit a profound impact on perturbing protein interactions, leading to human disease. However, predicting the effect of single mutations on protein interactions remains a major computational challenge. Deep learning, particularly protein language models or transformers, has become an effective tool in bioinformatics for protein structure prediction. However, the functional divergence of mutations makes it difficult to predict their interaction perturbation profiles. To address this fundamental challenge, we present eSIG-Net (edgetic mutation Sequence-based Interaction Grammar Network), a novel sequence-based "Interaction Language Model" for predicting protein interaction alterations caused by single mutations. eSIG-Net combines various protein sequence embeddings, introduces a mutation-encoding module with syntax and evolutionary insights, and employs contrastive learning to evaluate mutation-induced interaction changes. eSIG-Net significantly outperforms current state-of-the-art sequence-based and structure-based prediction methods at predicting mutational impact on protein interactions. We highlight examples where eSIG-Net nominates causal variants with high confidence and elucidates their functional role under relevant biological contexts. Together, eSIG-Net is a first-in-kind "interaction language model" that can accurately predict interaction-specific rewiring by single mutations with only sequence information, and exhibits generalizability across biological contexts.

bioinformatics↗

bioRxiv2025

Protein structure shapes natural genetic variation and de novo adaptation

Protein structural context strongly influences the functional outcomes of mutations, but exploiting this intuition to interpret the consequences of natural variants has been limited by the paucity of structural information. Here, we show that simple molecular heuristics based on predicted protein structures-solvent accessibility and the local complexity of the protein fold-are strong predictors of protein-coding variation in genomes from yeast to plants to humans. Polymorphisms in structured and unstructured regions alike were subject to these constraints, revealing fine-grained selection across amino acid residues and secondary structures. The same analyses distinguished deleterious variants in datasets from existing deep mutational scans. Extending the metrics to de novo adaptation, we developed a massively parallel directed evolution platform that isolated hundreds of independent adapted lineages within days. Optimized experimental conditions revealed dozens of rapamycin-resistant alleles of the FPR1/FKBP gene in a single experiment-resistance mutations that matched predictions from our structural heuristics. Together, these data demonstrate the power of a biochemical perspective to contextualize the functional landscape of both existing and newly arising genetic variation.

evolutionary biology↗

bioRxiv2025

Towards CRISPR-based editing of the mitochondrial genome in yeast

Mitochondria, which evolved from symbiotic bacteria, possess their own genomes (mtDNA) and support independent transcription and translation within the organelle. Given the essential role of mtDNA in energy production, metabolism, as well as cellular homeostasis, and the high density of confirmed pathogenic mutations that map to mtDNA, there is a pressing need for versatile methods to study and manipulate this genome. Although CRISPR technology has revolutionized the editing of nuclear genomes, it has not been successfully extended to mtDNA, primarily due to the challenge of delivering single guide RNAs (sgRNAs) across both outer and inner mitochondrial membranes. Here we develop a survival-based reporter in Saccharomyces cerevisiae to screen for potential RNA import motifs. We identify a 40-nucleotide aptamer (IM83) that facilitates sgRNA entry into the mitochondrial matrix, enabling CRISPR editing by a mitochondrially-localized adenine base editor. We show that mitochondrial import of IM83 is ATP-dependent and enhanced by the tRNA synthetase Msk1. Further investigations identify barriers to efficient CRISPR editing of mtDNA, including loss of membrane potential associated with mitochondrial targeting of the base editor. These insights lay the groundwork for future improvements in CRISPR-based editing of mtDNA in eukaryotes.

genetics↗

bioRxiv2025

A default silencing mechanism restrains stress-induced genes in C. elegans

Inducible gene expression programs require that target genes remain silent until the proper activation signal is received, a hallmark of stress-response pathways. This quiescence is typically assumed to be the default state of stress-inducible genes, maintained without active cellular intervention. Using a forward genetic screen for constitutive activation of inducible heat shock proteins (iHSPs) in C. elegans, we found that the multi-zinc-finger protein ZNF-236 is essential for maintaining iHSP quiescence under normal conditions. Loss of znf-236 causes constitutive iHSP expression throughout the genome, affecting both endogenous iHSP loci and iHSP sequences inserted at dispersed chromosomal sites. However, the effect is also chromosomal context-dependent: robustly heat-responsive iHSP transgenes integrated into the ribosomal DNA locus or extrachromosomal arrays are unaffected by znf-236 loss. This differential responsiveness suggests iHSP induction in znf-236 mutants results from a shift in genome organization, rather than from accumulated denatured proteins or engagement of the canonical heat shock response. Our findings demonstrate the existence of a potent ZNF-236-dependent default silencing mechanism that broadly restrains iHSP genes across the genome and helps ensure appropriate iHSP quiescence even at ectopic chromosomal locations. Contrary to prior assumptions, this suggests that quiescence of stress-inducible genes reflects an actively maintained genomic state rather than merely a passive absence of expression. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/683740v3_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@76b062org.highwire.dtl.DTLVardef@360ac9org.highwire.dtl.DTLVardef@1fe330eorg.highwire.dtl.DTLVardef@1c9ea7d_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2024

Stress-driven emergence of heritable non-genetic drug resistance

Drug resistance is the chief cause of treatment failure for therapies targeting chronic and infectious diseases. Whether the emergence of resistance is accelerated by environmental exposure to low levels of therapeutics remains controversial. Here, we report a non-genetic mechanism of stress adaptation that promotes heritable resistance to the widely used antifungal drug fluconazole. In the human fungal pathogen Candida albicans, transient exposure to subtherapeutic fluconazole doses induces a protective response that we term para-resistance. Like conventional resistance mechanisms, para-resistance is heritable. However, it does not arise from genetic mutations and can revert spontaneously. Systematic analyses of para-resistant isolates suggest that its key regulators include the stress-activated MAP kinase Hog1, the histone deacetylase subunit Snt1, the chromatin regulator Rap1, and the Sko1 transcriptional factor. Notably, molecules that disrupt biomolecular condensation and prion propagation - crucial for the inheritance of protein assemblies - block the induction of para-resistance, whereas inhibiting histone deacetylases facilitates its induction. We find that para-resistance is common in clinical isolates and, remarkably, passage through the mammalian gut triggers its acquisition, compromising fluconazoles therapeutic efficacy. Our work defines a pervasive, prion-like epigenetic mechanism of stress adaptation and highlights potential strategies to mitigate the rapid emergence of drug resistance.

microbiology↗

bioRxiv2024

Massively parallel experimental interrogation of natural variants in ancient signaling pathways reveals both purifying selection and local adaptation

The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and nearly neutral theories or whether they can commonly have large functional and fitness effects as proposed by the balance theory. We address this question by mapping the fitness effects of over 9,000 natural variants in the Ras/PKA and TOR/Sch9 pathways--key regulators of cell proliferation in eukaryotes--across four conditions in Saccharomyces cerevisiae. While most variants are neutral in our assay, [~]3,500 exhibited significant fitness effects. These non-neutral variants tend to be missense and to affect conserved, more densely packed, and less solvent-exposed protein regions. While some of these non-neutral variants are younger and rarer, and more often found in heterozygous states--consistent with purifying selection--a substantial fraction is present at high frequencies in the population, which is expected under balancing selection. Indeed, we find that variants with a positive fitness effect in our laboratory measurement show strong signs of local adaptation as they tend to be found specifically in domesticated strains isolated from human-made environments. Our findings support the view that while many common variants might be effectively neutral, a significant proportion have locally adaptive functional consequences and are driven into a subset of the population by local positive selection. This study highlights the potential to combine high-throughput precision genome editing with fitness measurements to explore natural genetic variation on a pathway-wide scale, thereby bridging the gap between population genetics and functional genomics to understand the nature of evolutionary forces in the wild.

evolutionary biology↗

bioRxiv2024

A genome-to-proteome atlas charts natural variants controlling proteome diversity and forecasts their fitness effects

Despite abundant genomic and phenotypic data across individuals and environments, the functional impact of most mutations on phenotype remains unclear. Here, we bridge this gap by linking genome to proteome in 800 meiotic progeny from an intercross between two closely related Saccharomyces cerevisiae isolates adapted to distinct niches. Modest genetic distance between the parents generated remarkable proteomic diversity that was amplified in the progeny and captured by 6,476 genotype-protein associations, over 1,600 of which we resolved to single variants. Proteomic adaptation emerged through the combined action of numerous cis- and trans-regulatory mutations, a regulatory architecture that was conserved across the species. Notably, trans-regulatory variants often arose in proteins not traditionally associated with gene regulation, such as enzymes. Moreover, the proteomic consequences of mutations predicted fitness under various stresses. Our study demonstrates that the collective action of natural genetic variants drives dramatic proteome diversification, with molecular consequences that forecast phenotypic outcomes. Highlights- Proteome diversity arises from natural genetic variants, with divergent proteomes in closely related parents and progeny. - Cis-regulatory elements had strong individual impacts, but coherent trans effects combined to dominate protein expression. - Directional selection and frequent transgression suggest much of the proteome is under selective pressure. - Many trans-regulators are enzymes or transporters, with fewer than 4% of pQTLs linking known interactors. - Genome-to-proteome connections predicted the fitness impact of mutations under various stresses, including a strong but hidden causal variant in IRA2/NF1.

systems biology↗

bioRxiv2024

Genes involved in protein folding and chromatin organization buffer genetic variation

Mutations are not always phenotypically active or show different effects in different individuals. While the mechanisms underlying this variable relationship between mutations and phenotypes are largely elusive, some specific genes may influence the phenotypic effects of cryptic variation. We employ the toolbox of Saccharomyces cerevisiae to perform a genome-wide screen aimed at identifying these so-called genetic buffer genes. Measuring the fitness of 1.8 million mutated strains identified a small set of evolutionary conserved buffer genes involved in protein folding and chromatin organization, including GIM3, SSA2, HOG1 and FKH2. Deletion of these genes increases the fitness effect of de novo mutations as well as standing genetic variation, with some mutations becoming adaptive. Moreover, losing a buffer gene results in a decline of standing genetic variation. Together, these results reveal a set of conserved genes that influence the phenotypic outcome of mutations and play a role in complex genetics and incomplete penetrance.

evolutionary biology↗

bioRxiv2023

Hsp90 shapes adaptation by controlling the fitness consequences of regulatory variation

The essential, stress-responsive protein chaperone Hsp90 impacts adaptation from microbes to humans. Yet the molecular mechanisms involved remain unclear and are often presumed to be driven by variation in opening reading frames. Here, we identify over 1,000 natural genotype-to-phenotype associations governed by Hsp90 at single-nucleotide resolution in Saccharomyces cerevisiae. Strikingly, cis-regulatory variants contributed to the chaperones effect on heredity more strongly than coding variation. Most of these mutations nonetheless impacted clients of Hsp90 or targets of its direct binding partners. The chaperones influence was especially potent on evolutionarily young genes, highlighting its influence on variation central to novelty. Synthetic reconstructions and genome editing revealed that Hsp90 may regulate the relationship between activity and phenotype for many dosage-sensitive genes. The unexpected role of the chaperone in buffering the effects of regulatory variants and releasing their consequences under stress suggests a mechanism for its widespread effects on evolution and development.

evolutionary biology↗

bioRxiv2023

Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells

Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how size influences cell physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be biochemically different. Here, we corroborate these results in mouse hepatocytes and extend our analysis using yeast. We find that size-dependent proteome changes are highly conserved and mostly independent of metabolic state. As eukaryotic cells grow larger, the dilution of the genome elicits a starvation-like proteome phenotype, suggesting that growth in large cells is limited by the genome in a manner analogous to a limiting nutrient. We also find that this phenomenon explains many proteomic changes ascribed to yeast aging. Overall, our data suggest that genome concentration is a universal determinant of proteome content in growing cells.

cell biology↗

bioRxiv2023

Compression of sickspan by interventions that steepen the survival curve

Longevity research aims to extend the period of healthy life, known as the healthspan, and to minimize the duration of disability and morbidity, known as the sickspan. Most longevity interventions in model organisms extend healthspan, but it is not known whether they extend healthspan relative to the lifespan - that is, whether they compress relative sickspan. Here, we present a theory that predicts which interventions effectively compress relative sickspan. The theory is based on the shape of the survival curve - the fraction of organisms surviving as a function of age. Interventions that extend mean lifespan while preserving the shape of the survival curve, known as scaling, are predicted to extend the sickspan proportionally, without compressing it. Such interventions include caloric restriction and many other longevity interventions. Conversely, a small subset of interventions that extend lifespan and steepen the shape of the survival curve, are predicted to compress the relative sickspan. We explain this based on the saturating removal mathematical model of aging, and present evidence from longitudinal health data in mice, Caenorhabditis elegans and Drosophila melanogaster. We discuss longevity interventions in mice that steepen the survival curves, including senolytics, ketogenic diet, and agents that reduce glucose spikes and protect blood vessels, as potential candidates for compressing the sickspan. We apply the theory to combinations of longevity interventions and discuss human healthspan data. This approach offers potential strategies for compressing morbidity and extending healthspan.

systems biology↗

bioRxiv2022

Identification of protein aggregates in the aging vertebrate brain with prion-like andphase separation properties

Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms mislocalized cytoplasmic aggregates in the brains of old killifish and mice. Interestingly, DDX5s prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the proteins ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline.

neuroscience↗

bioRxiv2022

Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate

Protein aggregation is a hallmark of age-related neurodegeneration. Yet, aggregation during normal aging and in tissues other than the brain is poorly understood. Here we leverage the African turquoise killifish to systematically profile protein aggregates in seven tissues of an aging vertebrate. Age-dependent aggregation is strikingly tissue-specific, and not simply driven by protein expression differences. Experimental interrogation, combined with machine learning, indicates that this specificity is linked to both protein-autonomous biophysical features and tissue-selective alterations in protein quality control. Co-aggregation of protein quality control machinery during aging may further reduce proteostasis capacity, exacerbating aggregate burden. A segmental progeria model with accelerated aging in specific tissues exhibits selectively increased aggregation in these same tissues. Intriguingly, many age-related protein aggregates arise in wild-type proteins that, when mutated, drive human diseases. Our data chart a comprehensive landscape of protein aggregation during aging and reveal strong, tissue-specific associations with dysfunction and disease. HIGHLIGHTSO_LITissue-specific protein aggregation is prevalent during vertebrate aging C_LIO_LIBoth protein biophysical properties and tissue-specific protein homeostasis patterns impact aggregation C_LIO_LIA segmental progeria model with accelerated aging exhibits selectively increased protein aggregation in affected tissues C_LIO_LIMany aggregates that accumulate during physiological aging are linked to disease C_LI

systems biology↗

bioRxiv2021

A Prion that regulates genome diversification

Epigenetic mechanisms mediate diverse gene expression programs in growth and development. Here we report a protein-based epigenetic element, a prion, formed by the conserved DNA helicase Mph1/FANCM. [MIX+] is a cytoplasmically inherited state with propagation driven by the non-amyloid prion templating of Mph1. [MIX+] provides resistance to DNA damage, a gain-of-function trait that requires helicase activity. [MIX+] reduces mitotic mutation rates, but promotes meiotic crossovers, driving measurable phenotypic diversification in wild outcrosses. Remarkably, [MIX+] can be induced by DNA-damaging stresses in which it is beneficial. Thus, [MIX+] fuels a quasi-Lamarckian form of inheritance that promotes survival of the current generation and diversification of the next.

molecular biology↗

bioRxiv2020

The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains

Prions are proteins capable of acquiring an alternate conformation that can then induce additional copies to adopt this same alternate conformation. Although initially discovered in relation to mammalian disease, subsequent studies have revealed the presence of prions in Bacteria and Viruses, suggesting an ancient evolutionary origin. Here we explore whether prions exist in Archaea - the last domain of life left unexplored with regard to prions. After searching for potential prion-forming protein sequences computationally, we tested candidates in vitro and in organisms from the two other domains of life: Escherichia coli and Saccharomyces cerevisiae. Out of the 16 candidate prion-forming domains tested, 8 bound to amyloid-specific dye, and six acted as protein-based elements of information transfer, driving non-Mendelian patterns of inheritance. We additionally identified short peptides from archaeal prion candidates that can form amyloid fibrils independently. Candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, suggesting that the presence of these amino acids may help distinguish functional prion domains from nonfunctional ones. Our data establish the presence of amyloid-forming prion-like domains in Archaea. Their discovery in all three domains of life further suggests the possibility that they were present at the time of the last universal common ancestor (LUCA). Significance StatementThis work establishes that amyloid-forming, prion-like domains exist in Archaea and are capable of vertically transmitting their prion phenotype - allowing them to function as protein-based elements of inheritance. These observations, coupled with prior discoveries in Eukarya and Bacteria, suggest that prion-based self-assembly was likely present in lifes last universal common ancestor (LUCA), and therefore may be one of the most ancient epigenetic mechanisms.

evolutionary biology↗

bioRxiv2019

A stress response that allows highly mutated eukaryotic cells to survive and proliferate

Rapid mutation fuels the evolution of many cancers and pathogens. Much of the ensuing genetic variation is detrimental, but cells can survive by limiting the cost of accumulating mutation burden. We investigated this behavior by propagating hypermutating yeast lineages to create independent populations harboring thousands of distinct genetic variants. Mutation rate and spectrum remained unchanged throughout the experiment, yet lesions that arose early were more deleterious than those that arose later. Although the lineages shared no mutations in common, each mounted a similar transcriptional response to mutation burden. The proteins involved in this response formed a highly connected network that has not previously been identified. Inhibiting this response increased the cost of accumulated mutations, selectively killing highly mutated cells. A similar gene expression program exists in hypermutating human cancers and is linked to survival. Our data thus define a conserved stress response that buffers the cost of accumulating genetic lesions and further suggest that this network could be targeted therapeutically.

genetics↗

bioRxiv2017

Epigenetic regulation of genome integrity by a prion-based mechanism

Epigenetic mechanisms mediate diverse gene expression programs in growth and development. Yet whether any can permanently alter the genome is unknown. Here we report a protein-based epigenetic element, a prion, formed by the conserved DNA helicase Mph1/FANCM. [MPH1+] provides resistance to DNA damage, a gain-of-function trait that requires helicase activity and interactions with other DNA repair proteins. Strikingly, the intrinsically disordered regions of Mph1 and human FANCM that are required for prion phenotypes do not resemble known prions. [MPH1+] reduces mitotic mutation rates, but promotes meiotic crossovers, driving phenotypic diversification in wild outcrosses. Remarkably, [MPH1+] is induced by stresses in which the prion is beneficial. Thus, [MPH1+] fuels a quasi-Lamarckian form of inheritance that promotes survival of the current generation and diversification of the next.

genetics↗