Biology subjects

Pilpel, Y. T.

Publications and source records attributed to Pilpel, Y. T..

11 recordsLinked to original sources

bioRxiv2026

A massively parallel reporter screen defines the syntax of SECReTE, a secretion-enhancing cis regulatory targeting element, in mammalian cells

Messenger RNA (mRNA) localization to specific subcellular regions is crucial for proper protein translation and localization. Potential means to localize mRNAs include cis-acting or structural motifs embedded within the sequence. We previously identified a secretion-enhancing cis regulatory targeting element (SECReTE) enriched in mRNAs encoding secreted proteins from prokaryotes, eukaryotes, and viruses, found to enhance both protein synthesis and secretion by localizing mRNAs to the endoplasmic reticulum (ER) membrane. Defined as at least 10 consecutive NNY triplets (where N is any nucleotide and Y is a pyrimidine), this highly degenerate motif can be specified by approximately ~10^15 different sequence combinations. Yet, some combinations may prove more efficient than others in regulating mRNA localization and protein secretion. To better understand SECReTE syntax and to identify robust combinations, we designed and synthesized a library of ~5 x 10^4 variants and inserted them into the 3' untranslated region (3'UTR) of two reporter genes, green fluorescent protein (GFP) and immunoglobulin light chain. We expressed each variant in Chinese hamster ovary cells and assayed their activity using parallel assays to measure the effect of each variant upon mRNA partitioning between the ER and cytoplasm, and protein secretion. Our results reveal that ER-associated mRNAs are enriched with SECReTE elements of a defined syntax. Notably, RRY repeats (where R is purine) were superior to NNY repeats. Variants conferring a high mRNA ER localization score consistently enhanced protein secretion, confirming the mechanistic relationship between mRNA targeting to the ER and secretion efficiency. The correlation between variant performances across both reporters suggests a shared regulatory mechanism. Additional analysis identified a novel secretion-promoting cis element, called "split NNS" (where S is G or C). This work refines the syntactic definition of mRNA localization motifs that regulate protein secretion in both natural and heterologous expression systems.

cell biology↗

bioRxiv2025

The evolutionary origin of host association and polycistronic transcription in trypanosomatids

Trypanosomatids (Kinetoplastids) encompass multiple lineages of parasitic protists with monoxenous or dixenous life cycles, infecting insects, vertebrates, and plants; in vertebrate hosts, some are intracellular, while others are extracellular. To understand the origin and diversification of their host associations, we integrated comparative genomics across 47 genomes. Results highlight that monoxenous, extracellular trypanosomatids originated from predatory ancestors through reductive evolution, which diminished their metabolic and hunting capabilities. Intracellularity and dixenous lifestyle convergently originated three times independently. Progressive consolidation of genes into polycistronic transcription units (PTUs) was a central innovation that began in early Glycomonada and expanded through chromosome fission-fusion and gene relocation/inversion. In present-day PTUs, protein complex subunits and metabolic pathway enzymes are positioned for co-expression in temporal synchrony, and chromosomes minimize colinear PTUs to counter transcriptional readthrough. Together, these results provide a time-resolved origin of host-association and polycistronic transcription in trypanosomatids, possibly through an intermediate phase of facultative parasitism.

evolutionary biology↗

bioRxiv2025

Encoded and non-genetic alternative protein variants expand human functional proteome

Each stage of the Central Dogma contributes to proteome diversity through mechanisms such as heterozygosity, somatic mutations, transcriptional errors, and translational errors. As a result, a diverse array of protein variants can coexist within a single proteome, such as that of humans. However, until now, methods to detect, quantify, and evaluate the functional consequences of these variants have been lacking. Here we examined a large-scale proteogenomic dataset from 29 healthy human tissues and uncovered 13,910 confidently localized variants representing 7,215 unique single amino acid substitutions co-existing alongside their corresponding reference proteoforms. We found that the abundance of both genetic (SNPs, somatic mutations) and mistranslated protein variants mirrors their allele frequencies in the human population. Moreover, we show that non-genetic substitutions may provide a distinct route for exploring protein sequence space, circumventing the mutational constraints imposed by the genetic code. In addition, we provide experimental validation of non-genetic substitution on selected purified proteins. We demonstrate specific and recurring non-genetic variation patterns upon amino acid starvation in proteome-wide analyses of cancer-derived cell lines and identify hundreds of substituted non-genetic proteoforms that recur consistently in multiple healthy individuals or map to annotated protein functional sites. We propose that these substitutions constitute a novel class of functional protein phenotypic variants. Collectively, our findings indicate that non-genetic amino acid substitutions in human proteins provide an abundant source to expanding the functional proteome.

molecular biology↗

bioRxiv2024

Adaptive Mate Selection in Saccharomyces cerevisiae Revealed Through a High-Throughput Mating Assay

In evolutionary biology, sexual mating plays a pivotal role in facilitating the combination of beneficial alleles among individuals. Cross-species data suggest that organisms selectively mate with partners based on factors such as genetic distance and partner fitness. Understanding the determinants of pair-specific mating affinity is crucial for unraveling the impact of sex on evolution. However, despite the significance of this phenomenon, the availability of large and consistent datasets is limited, leading to inconsistent conclusions. To address this gap, we present a comprehensive mating assay enabling the simultaneous quantification of mating affinity among approximately 100 natural Saccharomyces cerevisiae strains. Our study demonstrates that mating in an en masse manner, allowing mating based on affinity, enhances the overall fitness of the hybrids offspring population compared to mating that enforces one specific partner at a time. By employing a DNA barcode recombination system integrated into natural isolates genomes, we sequence recombined barcode pairs and revealed mating frequencies and affinities among all strains in different environments. Our findings unveil strain-specific mating affinity among natural yeast strains, with certain parental pairs exhibiting a heightened affinity for each other over other strains, whereas certain strains combinations are avoided. Notably, among the pairs with the highest affinity, there is a preference for lower genetic distances. Intriguingly, multiple strains show a propensity for mating with partners that yield higher-fitness hybrids on average. Collectively, our results provide compelling evidence that yeast actively engages in adaptive mate affinity.

evolutionary biology↗

bioRxiv2024

Quantitative genetics of natural S. cerevisiae strains upon sexual mating reveals heritable determinants of cellular fitness

Quantitative genetics requires large datasets of diverse phenotyped-genotyped strains from the same species. A special need is for such archived biological material and computerized data in sexually reproducing individuals from a species. Here we leverage sexual mating among close to 100 diverse natural isolates of the yeast S. cerevisiae that form about 4,000 hybrids combinations in several ecologically relevant growth conditions. In a first genetic study of this new resource we focus on fitness measurements and its modes of inheritance as a quantitative trait from parents to offspring hybrids. We employ genomic barcoding of all strains and a barcode recombination technique to follow hybrids of each successful mate combination. For all parents, and separately for all offspring hybrids we measure fitness under each condition. We focus on the inheritance of fitness, the ultimate evolutionary trait, and its inheritance as a quantitative trait upon sexual mating. Predicting hybrid fitness given parental parameters is a major challenge as it is likely multi-factorial. We find that hybrids fitness in fermentable carbon source correlates positively, yet modestly, with parental fitness, while on non-fermentable carbon, hybrid fitness shows no detectable correlation with parental fitness. Instead, the non-fermentable condition, hybrid fitness increases sharply with genetic distance between their parents, suggesting that outbreeding maximizes fitness irrespective of parental fitness at that condition. The number of minor alleles in the genome of each hybrid, analogous to polygenic risk score in classical genetics, negatively correlates with fitness in both conditions. Fitness inheritance can be explained by either a dominance or a co-dominance modes of inheritance, in the non-fermentable and fermentable conditions respectively. Our newly suggested biological resource and data provide new foundations for a quantitative research in genetics and evolution upon sexual mating. Furthermore, our barcoded strains and mating tracking method provide an important research resource for the yeast community.

genetics↗

bioRxiv2024

Competitive fungal commensalism mitigates candidiasis pathology

The mycobiota are a critical part of the gut microbiome, but host-fungal interactions and specific functional contributions of commensal fungi to host fitness remain incompletely understood. Here we report the identification of a new fungal commensal, Kazachstania heterogenica var. weizmannii, isolated from murine intestines. K. weizmannii exposure prevented Candida albicans colonization and significantly reduced the commensal C. albicans burden in colonized animals. Following immunosuppression of C. albicans colonized mice, competitive fungal commensalism thereby mitigated fatal candidiasis. Metagenome analysis revealed K. weizmannii presence among human commensals. Our results reveal competitive fungal commensalism within the intestinal microbiota, independent of bacteria and immune responses, that could bear potential therapeutic value for the management of C. albicans-mediated diseases.

immunology↗

bioRxiv2022

Evolutionary safety of death by mutagenesis

Nucleoside analogs are a major class of antiviral drugs. Some act by increasing the viral mutation rate causing "death by mutagenesis" of the virus. Their mutagenic capacity, however, may lead to an evolutionary safety concern. We define evolutionary safety as a probabilistic assurance that the treatment will not generate an increased number of epidemiologically concerning mutated virus progeny. We develop a mathematical framework to estimate the total mutant load produced with and without mutagenic treatment. We predict rates of appearance of virus mutants as a function of the timing of treatment and the immune competence of patients, employing various assumptions about the vulnerability of the viral genome and its potential to generate undesired phenotypes. We focus on the case study of Molnupiravir, which is an FDA-approved treatment against COVID-19. We estimate that Molnupiravir is narrowly evolutionarily safe, subject to the current estimate of parameters. Evolutionary safety can be improved by restricting treatment to individuals with a low clearance rate and by designing treatments that lead to a greater increase in mutation rate. We report a simple rule to determine the fold-increase in mutation rate required to obtain evolutionary safety which is also applicable to other pathogen-treatment combinations.

evolutionary biology↗

bioRxiv2021

Fitness landscape analysis reveals that the wild type allele is sub-optimal and mutationally robust

Fitness landscape mapping and the prediction of evolutionary trajectories on these landscapes are major tasks in evolutionary biology research. Evolutionary dynamics is tightly linked to the landscape topography, but this relation is not straightforward. Here, we analyze a fitness landscape of a yeast tRNA gene, previously measured under four different conditions. We find that the wild type allele is sub-optimal, and 8%-10% of its variants are fitter. We rule out the possibilities that the wild type is fittest on average on multiple conditions or located on a local fitness maximum. Instead, we find that the wild type is mutationally robust ( flat), while more fit variants are typically mutationally fragile. Similar observations of mutational robustness or flatness have been so far made in very few cases, predominantly in viral genomes.

evolutionary biology↗

bioRxiv2021

Epigenetically Inherited Mutation Rates Predicted to Maximize Adaptation Rates

Mutation rate plays an important role in adaptive evolution due to its effect on the rate of appearance of both beneficial and deleterious mutations and is therefore subject to second-order selection. The mutation rate varies between and within species and populations, increases under some stresses, and can be modified by mutator and anti-mutator alleles. It may also vary among genetically identical individuals: empirical evidence from bacteria suggests that the mutation rate can be affected by translation errors and expression noise in various proteins. Importantly, this non-genetic variation may be heritable via a transgenerational epigenetic mode of inheritance, giving rise to mutator phenotype switching that is independent from mutator alleles. Here we investigate mathematically how the rate of adaptive evolution on rugged, complex fitness landscapes is affected by the rate of mutation rate phenotype switching. Motivated by recent experimental results of mutation rate variation, we model an asexual population with two mutation rate phenotypes, non-mutator and mutator. An offspring may switch from its parental phenotype to the other phenotype. Thus, the mutation rate can be interpreted as a genetically inherited trait when the switching rate is low, as an epigenetically inherited trait when the switching rate is intermediate, or as a randomly determined trait when the switching rate is high. We find that intermediate switching rates maximize the rate of adaptation on rugged fitness landscapes. This is because an intermediate switching rate can maintain within the same individuals both a mutator phenotype and pre-existing mutations, a combination that facilitates the crossing of fitness valleys. Further, intermediate switching rates allow the population to quickly revert to a low mutation rate after adaptation is achieved, avoiding the accumulation of deleterious mutations linked to mutator alleles. Our results rationalize recently observed noise in the expression of proteins that affect the mutation rate and suggest that non-genetic inheritance of this phenotype may facilitate evolutionary adaptive processes.

evolutionary biology↗

bioRxiv2020

Manipulation of the human tRNA pool reveals distinct tRNA sets that act in cellular proliferation or cell cycle arrest

Different subsets of the tRNA pool in human are expressed in different cellular conditions. The "proliferation-tRNAs" are induced upon normal and cancerous cell division, while the "differentiation tRNAs" are active in non-dividing, differentiated cells. Here we examine the essentiality of the various tRNAs upon cellular growth and arrest. We established a CRISPR-based editing procedure with sgRNAs that each target a tRNA family. We measured tRNA essentiality for cellular growth and found that most proliferation tRNAs are essential compared to differentiation tRNAs in rapidly growing cell lines. Yet in more slowly dividing lines, the differentiation tRNAs were more essential. In addition, we measured these tRNAs roles upon response to cell cycle arresting signals. Here we detected a more complex behavior with both proliferation-tRNAs and differentiation tRNAs showing various levels of essentiality. These results provide the so-far most comprehensive functional characterization of human tRNAs with intricate roles in various proliferation states.

molecular biology↗

bioRxiv2020

Dynamic changes in tRNA modifications and abundance during T-cell activation

The tRNA pool determines the efficiency, throughput, and accuracy of translation. Previous studies have identified dynamic changes in the tRNA supply and mRNA demand during cancerous proliferation. Yet, dynamic changes may occur also during physiologically normal proliferation, and these are less characterized. We examined the tRNA and mRNA pools of T-cells during their vigorous proliferation and differentiation upon triggering their antigen receptor. We observe a global signature of switch in demand for codons at the early proliferation phase of the response, accompanied by corresponding changes in tRNA expression levels. In the later phase, upon differentiation, the response of the tRNA pool is relaxed back to basal level, potentially restraining excessive proliferation. Sequencing of tRNAs allowed us to also evaluate their diverse base-modifications. We found that two types of tRNA modifications, wybutosine and ms2t6A, are reduced dramatically during T-cell activation. These modifications occur in the anti-codon loops of two tRNAs that decode "slippery codons", that are prone to ribosomal frameshifting. Attenuation of these frameshift-protective modifications is expected to increase the potential for proteome-wide frameshifting during T-cell proliferation. Indeed, human cell lines deleted of a wybutosine writer showed increased ribosomal frameshifting, as detected with a HIV gag-pol frameshifting site reporter. These results may explain HIVs specific tropism towards proliferating T-Cells since it requires ribosomal frameshift exactly on the corresponding codon for infection. The changes in tRNA expression and modifications uncover a new layer of translation regulation during T-cell proliferation and exposes a potential trade-off between cellular growth and translation fidelity. Significance statementThe tRNA pool decodes genetic information during translation. As such, it is subject to intricate physiological regulation in all species, across different physiological conditions. Here we show for the first time a program that governs the tRNA pool and its interaction with the transcriptome upon a physiological cellular proliferation- T-cells activation. We found that upon antigenic activation of T-cells, their tRNA and mRNA pools undergo coordinated and complementary changes, which are relaxed when cells reduce back their proliferation rate and differentiate into memory cells. We found a reduction in two particular tRNA modifications that have a role in governing translation fidelity and frameshift prevention. This exposes a vulnerability in activated T-cells that may be utilized by HIV for its replication. ClassificationBIOLOGICAL SCIENCES; cell biology

genomics↗