Biology subjects

DeLuna, A.

Publications and source records attributed to DeLuna, A..

16 recordsLinked to original sources

bioRxiv2026

Chronological lifespan correlates with virulence within Candida albicans but long lifespan is not restricted to pathogenic Candida species

Yeast cells can remain viable for extended periods after entering stationary phase, a survival trait measured as chronological lifespan (CLS). Although CLS is well characterized in Saccharomyces cerevisiae as a model of postmitotic aging, its relevance to human-associated fungi remains poorly understood. Candida species of the CTG (CUG-Ser1) clade vary widely in ecology and clinical importance, raising the question of whether stationary-phase survival is linked to pathogenicity across species or among strains. Here, we combine an optimized CFU-based CLS assay with scalable flow cytometry of membrane integrity across Candida species and genetically diverse Candida albicans isolates. CLS varies extensively across species, yet caloric restriction extends survival in every species examined, revealing a remarkably consistent response to reduced glucose despite marked differences in baseline lifespan. Pathogenic species tend toward longer CLS, but long lifespan is not restricted to them, with the non-pathogenic C. sojae among the longest-lived species examined. Among 20 genetically diverse C. albicans clinical isolates, longer CLS is consistently associates with greater virulence. Our study establishes a methodological framework for comparative CLS analysis, reveals a broadly shared response to caloric restriction, and shows that the association between CLS and virulence emerges within C. albicans but not across Candida species.

microbiology↗

bioRxiv2026

Domestication and deep lineage divergence define two discrete trajectories in Kluyveromyces marxianus

Although genomics has greatly improved our ability to detect population structure and genetic divergence, it remains difficult to determine when diversity within a recognized species reflects continuous variation and when it marks the emergence of discrete evolutionary lineages. In yeasts, population-genomic studies often reveal overlapping signatures of environmental association, admixture, and domestication, making this distinction especially challenging. By analyzing 178 globally sampled genomes from Kluyveromyces marxianus, an emerging yeast of biotechnological interest, we show that diversity within this species resolves into two contrasting evolutionary trajectories that do not map onto broad geographic origin. Most industrial and clinical isolates belong to a lineage marked by gene loss, aneuploidy, and reduced fertility, consistent with genomic hallmarks of domestication. In contrast, isolates confined to traditional agave fermentations in Mexico and South Africa form a highly distinct lineage, separated from the other lineages by up to 4.8% genome-wide nucleotide divergence, widespread reciprocal monophyly, no detectable recent gene flow, and reduced mating compatibility despite co-occurrence with other lineages. Together, these results show that within a single yeast species, domestication-associated genome remodeling and deep lineage divergence can define distinct trajectories, with implications for strain selection in biotechnology.

evolutionary biology↗

bioRxiv2025

SWR1C loss promotes longevity through tRNA-mediated proteostasis

The conserved SWR1C chromatin remodeling complex promotes cellular aging, yet the mechanisms linking its activity to lifespan control remain poorly defined. Although SWR1C shapes chromatin architecture and regulates non-coding RNA expression, how these activities relate to its role in aging remains unclear. Here, we combine genetic and lifespan-epistasis analyses to identify the cellular processes that underlie SWR1C-dependent chronological longevity in Saccharomyces cerevisiae. Loss of subunits specifically required for H2A.Z deposition robustly extends longevity, and this effect is functionally linked to cytosolic translation and proteostasis pathways. Lifespan profiling of ncRNA deletions reveals a substantial fraction of aging phenotypes and prevalent genetic interactions with SWR1, with tRNAs emerging as key determinants of its long-lived phenotype. The expression of specific tRNA genes is dysregulated in swr1{Delta} cells, and interactions with tyrosine-decoding tRNA genes are linked to ER proteotoxic stress, suggesting that altered tRNA pools affect proteostasis during aging. These findings establish tRNAs as central mediators of SWR1C-associated longevity, revealing a fundamental connection between chromatin remodeling, RNA biology, and proteostasis stress responses in lifespan regulation.

cell biology↗

bioRxiv2025

Hanseniaspora yeasts from agave fermentations provide insight into intraspecific gene loss

Hanseniaspora species stand out among yeasts for having the smallest genomes, marked by extensive gene family contractions. Consequently, they have been proposed as model organisms for studying the evolution of free-living cells lacking genes otherwise considered essential. Here, we show that Hanseniaspora yeasts are prevalent in agave fermentations used to produce traditional spirits across Mexico. We sequenced the genomes of 15 strains, unambiguously identifying them as H. lachancei, H. pseudoguilliermondii, H. guilliermondii, and H. opuntiae. Comparative genomic analyses revealed dynamic shifts in gene family sizes and compositions, suggesting ongoing gene loss within the fast-evolving branch of this genus. Notably, gene losses varied across functional categories, even among isolates of the same species. Growth assays across diverse stress conditions and carbon sources indicated that these genomic disparities do not directly translate into phenotypic differences. Together, our findings suggest that differential gene loss within species is an active evolutionary process shaping Hanseniaspora genomes, highlighting agave-fermentation populations as valuable models for studying genome reduction in a natural context.

genomics↗

bioRxiv2025

Metformin-induced longevity is associated with retrotransposon dynamics in yest chronological aging

The widely used antidiabetic drug metformin extends lifespan across diverse model organisms, from yeast to primates. However, the cellular mechanisms underlying its anti-aging effects remain only partially understood. Here, we combined large-scale genetic screening and high-resolution lifespan phenotyping with transcriptomic and proteomic analyses to provide a systems view of metformins impact on the chronological lifespan of Saccharomyces cerevisiae. Unexpectedly, we uncovered pronounced gene-drug interactions between metformin and chromatin-modifying factors. Specifically, deletions of Set3C histone deacetylation complex subunits phenocopied the longevity effect of metformin, with no additive benefit when combined, suggesting convergence on shared pathways. Transcriptome profiling further revealed that metformin reprogrammed stationary-phase gene expression, with Ty1-copia retrotransposons emerging as a consistently induced signature, thereby suggesting a possible mechanism for the observed interactions with Set3C regulation. Paradoxically, TYA Gag-like protein levels and retrotransposition frequency were modestly reduced, indicating an uncoupling between transcriptional activation and retromobility. Proteome analysis revealed increased abundance of mitochondrial and stress-response proteins as primary outcomes of metformin exposure, both known modulators of Ty1 dynamics in yeast. Together, our findings position chromatin regulation and retrotransposon expression as integral components of metformins pro-longevity mechanisms, expanding its influence beyond signaling, metabolism, and stress response. HighlightsO_LILarge-scale genetic screening reveals that deletions of Set3C histone deacetylase phenocopy metformin-induced longevity. C_LIO_LIMetformin consistently induces Ty1 retrotransposon transcription but reduces Gag protein abundance and retromobility. C_LIO_LIProteomic changes highlight mitochondrial and stress-response proteins as primary outcomes of metformin exposure. C_LIO_LIRetrotransposon dynamics emerge as a key component associated with metformin-induced longevity. C_LI

cell biology↗

bioRxiv2025

Ecological divergence of sympatric Saccharomyces species across wild and fermentative environments in the neotropics

The common yeast Saccharomyces cerevisiae is widely associated with anthropogenic habitats and dominates agave fermentations in Mexico, despite the absence of starter cultures in artisanal production. Yet, the origins and dispersal of the microorganisms involved in this fermentation system--including wild S. cerevisiae and its sister species S. paradoxus--remain poorly understood. Here, we analyzed the distribution of these two species across three regions in Mexico by collecting a total of 861 samples from 15 traditional distilleries and 25 nearby natural sites, including tree bark, insects, fermentation tanks, and distillery surfaces. Among 4,006 isolates identified by MALDI-TOF biotyping, S. cerevisiae and S. paradoxus were recovered at overall rates of 21% and 3.4%, respectively, with the former more frequently found in distilleries and the latter in natural habitats. Notably, Saccharomyces isolates were not exclusively associated with oak trees, as strains were also recovered from leguminous, pine, and Anacardiaceae trees, suggesting that the oak specialization observed in temperate regions may not hold in tropical environments. Genome sequencing of 100 Saccharomyces isolates and SNP-based analyses showed that S. cerevisiae strains clustered by geography, not by substrate, and were largely confined to two Mexican Agave clades, with minor representation from the North American Oak, Pacific West Coast, and Wine clades. Strains isolated from agave fermentations belonged to the same populations as those from plant substrates, with insects, especially Drosophilidae, likely mediating their dispersal. Meanwhile, S. paradoxus isolates grouped into the SpA (Eurasian) and SpB (North American) lineages, with three novel SpB subclades identified. Intriguingly, one of these, the SpB_MxAgave population, was exclusively associated with agave fermentations, providing the first evidence of a persistent association of S. paradoxus with an anthropogenic habitat. Our study sheds light on the ecological dynamics and diversity of S. cerevisiae and S. paradoxus populations in the neotropics.

microbiology↗

bioRxiv2025

Regulation of the branched-chain amino acid pathway and its crosstalk to carbon metabolism in yeast

In Saccharomyces cerevisiae, the TORC1 pathway regulates the transition from rapid fermentative growth to respiration during the diauxic shift, by tightly coordinating energy- and biomass-producing pathways. Although leucine and other components of the branched-chain amino acid (BCAA) pathway are known TORC1 regulators, how the BCAA pathway is controlled across this transition and influences the crosstalk between central carbon and amino acid metabolism remains unclear. By integrating high-throughput flow cytometry and untargeted LC-MS metabolomics into a thermodynamically curated genome-scale model, we profiled protein levels, metabolite dynamics, and cellular context during the diauxic shift of a GFP-tagged strain library of the BCAA pathway in wild-type and mutants lacking non-essential genes for BCAA biosynthesis. This analysis revealed that the BCAA pathway operates in two branches, with only the leucine-committed branch exhibiting a fermentative signature aligned with TORC1 activity. We further identified key regulatory elements and showed that dysregulation of the BCAA pathway disrupts distant metabolic circuits, including central carbon metabolism. Our findings highlight the dynamic role of the BCAA pathway in metabolic network integration during the diauxic shift.

systems biology↗

bioRxiv2025

Exposing the core genetic drivers of chronological aging in yeast cells

The chronological lifespan of Saccharomyces cerevisiae has been pivotal in advancing our understanding of aging in eukaryotic cells. However, gaining a genome-wide perspective of this trait remains challenging due to substantial discrepancies observed across large-scale gene-deletion screens. In this study, we performed a meta-analysis to compile a ranked catalog of key processes and regulators driving chronological longevity in yeast, ensuring their robustness across diverse experimental setups. These consistent chronological aging factors were enriched in genes associated with yeast replicative lifespan and orthologs implicated in aging across other model organisms. Functional analysis revealed that the downstream cellular mechanisms underlying chronological longevity in yeast align with well-established, universal hallmarks of aging, underscoring the potential of the yeast chronological aging model to investigate conserved aging processes. Additionally, we identified transcriptional regulators associated with these consistent genetic factors, uncovering potential global and local modulators of chronological aging. Among these, Tec1, a key regulator of the filamentous growth pathway, emerged as a central hub connected to multiple aging pathways. To further elucidate the functional role of this regulator, we conducted a high-resolution lifespan-epistasis screen, demonstrating that TEC1 and mitochondrial machinery promote chronological longevity in parallel, compensating for each others impaired functions. Our findings provide an integrated view of the core genetic and functional landscape underlying aging in yeast cells.

genetics↗

bioRxiv2024

Recurrent introgression and geographical stratification shape Saccharomyces cerevisiae in the Neotropics

HighlightsO_LIPhylogenetic analyses of S. cerevisiae isolates from agave fermentation reveal novel clades within the Neotropical cluster. C_LIO_LIThe Neotropical cluster shows geographical population structure. C_LIO_LIMultiple pulses of interspecific introgression are part of the evolutionary history of S. cerevisiae in the Neotropics C_LI From yeasts to humans, introgressive hybridization significantly influences the evolutionary history of living organisms by introducing new genetic diversity. Strains of Saccharomyces cerevisiae worldwide exhibit introgressions from the sister species S. paradoxus, despite the average sequence identity between these species being lower than 90%. While S. cerevisiae isolates from the Neotropics are known for their high levels of introgression, the evolutionary events leading to the unusually high prevalence of them remain unclear. Here, we sequenced 216 S. cerevisiae isolates living in open agave fermentation across Mexico, a habitat at the interface of natural and industrial environments. The genomes of these strains revealed considerable genetic diversity and population structure linked to geographic distribution, which had been overlooked due to undersampling of this megadiverse region. These strains, along with those from French Guiana, Ecuador, and Brazil, form a broader Neotropical phylogenetic cluster that is notably enriched in introgressed DNA. Surprisingly, the origins and conservation patterns of introgressions indicate multiple hybridization events, suggesting an unprecedented scenario of flexible species barriers in this region. Our findings underscore concurrent evolutionary processes--geographical stratification and multiple introgressions--that shape the genomes of a diverse lineage of S. cerevisiae. Neotropical yeasts thus provide a natural laboratory for exploring the mechanisms and adaptive significance of introgressive hybridization in eukaryotic genome evolution.

evolutionary biology↗

bioRxiv2024

Microbial communities thriving in agave fermentations are locally influenced across diverse biogeographic regions

The production of traditional agave spirits in Mexico is a deeply rooted traditional process that relies on environmental microorganisms to ferment the cooked must from agave plants. Analysis of these microorganisms provides the opportunity to understand the dynamics of the microbial communities in the interface of natural and human-associated environments in a biologically and culturally rich region of the world. Here, we performed 16S and ITS amplicon sequencing of close to 100 fermentation tanks from 42 distilleries throughout Mexico. The Agave species used, production practices, climatic conditions, and biogeographic characteristics varied considerably among sites. Yet, we did find taxa present in most fermentations suggesting that there is a core of microorganisms that are hallmarks of these communities. These core taxa are represented by hundreds of OTUs showing large intra-specific variation. The only variable that was consistently associated with the composition of both bacterial and fungal communities was the distillery, suggesting that microbial composition is determined by the local production practices and unique attributes of each site. Fermentation stage, climate and producing region were also associated with the community composition, but only for prokaryotes. Analysis of microbial composition in several tanks within three distilleries also revealed taxa that were enriched in specific fermentation stages or agave species. Our work provides a comprehensive analysis of the microbiome of agave fermentations, contributing key knowledge for its management and conservation.

microbiology↗

bioRxiv2023

Yeast diversity in open agave fermentations across Mexico

Yeasts are a diverse group of fungal microorganisms that are widely used to produce fermented foods and beverages. In Mexico, open fermentations are used to obtain spirits from agave plants. Despite the prevalence of this traditional practice throughout the country, yeasts have only been isolated and studied from a limited number of distilleries. To systematically describe the diversity of yeast species from open agave fermentations, here we generate the YMX.1.0 culture collection by isolating 4,524 strains from 68 sites in diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and a subset of the strains was verified by ITS and D1/D2 sequencing. The most abundant species isolated from all producing regions were Saccharomyces cerevisiae, Pichia kudriavzevii, Pichia manshurica, and Kluyveromyces marxianus. Despite the great diversity of environmental conditions and production practices the composition of yeast communities remained largely homogeneous throughout locations and fermentation stages, even if less abundant but commonly occurring yeasts were considered. Furthermore, ITS and D1/D2 sequencing revealed two candidate new species of Saccharomycetales. To explore the intraspecific variation of the yeasts from agave fermentations, we conducted genome sequencing on four isolates of the non-conventional yeast Kazachstania humilis. The genomes of these four strains were considerably distinct from other genomes of the same species, suggesting that they belong to a different population. Our work contributes to the understanding and conservation of an open fermentation system of great cultural and economic importance, providing a valuable resource to study the biology and genetic diversity of microorganisms living at the interface of natural and human-associated environments. TAKE AWAYO_LIWe isolated and identified 4,524 yeast strains from open agave fermentations in Mexico. C_LIO_LIYeast communities remained largely homogeneous throughout diverse locations. C_LIO_LIKazachstania humilis genomes differed significantly from isolates in other regions of the world. C_LIO_LIWe report two candidate new species related to the Pichia clade. C_LI

microbiology↗

bioRxiv2022

Genomewide identification of subtelomeric silencing factors in budding yeast

Subtelomeric gene silencing is the negative transcriptional regulation of genes located close to telomeres. This phenomenon occurs in a variety of eukaryotes with salient physiological implications, such as cell adherence, virulence, immune-system escape, and aging. The process has been widely studied in the budding yeast Saccharomyces cerevisiae, where genes involved in this process have been identified mostly on a gene-by-gene basis. Here, we introduce a quantitative approach to study subtelomeric gene silencing, that couples the classical URA3 reporter with GFP monitoring, amenable to high-throughput flow cytometry analysis. This reporter was integrated into several subtelomeric loci in the genome, where it showed a gradual range of silencing effects. By crossing strains with this dual reporter at the COS12 and YFR057W subtelomeric query loci with gene-deletion mutants, we carried out a genome-wide, comprehensive screen for subtelomeric-silencing factors. The approach was replicable and allowed detection of expression changes caused by previously described silencing factors. We also identified new molecular players affecting this process, most of which are related to functions underlying chromatin conformation. This was the case of LGE1, a novel silencing factor herein reported, associated with histone ubiquitination. Our strategy can be readily combined with other reporters and gene perturbation collections, making it a versatile tool to study gene silencing at a genome-wide scale.

genetics↗

bioRxiv2019

A Competitive-Aging Method for Quantitative Genetic Analysis of the Chronological Lifespan of Saccharomyces cerevisiae

The chronological lifespan of budding yeast is a model of aging and age-related diseases. This paradigm has recently allowed genome-wide screening of genetic factors underlying post-mitotic viability in a simple unicellular system, which underscores its potential to provide a comprehensive view of the aging process. However, results from different large-scale studies show little overlap and typically lack quantitative resolution to derive interactions among different aging factors. We previously introduced a sensitive, parallelizable approach to measure the chronological-lifespan effects of gene deletions based on the competitive aging of fluorescence-labeled strains. Here, we present a thorough description of the method, including an improved multiple-regression model to estimate the association between death rates and fluorescent signals, which accounts for possible differences in growth rate and experimental batch effects. We illustrate the experimental procedure--from data acquisition to calculation of relative survivorship--for ten deletion strains with known lifespan phenotypes, which is achieved with high technical replicability. We apply our method to screen for gene-drug interactions in an array of yeast deletion strains, which reveals a functional link between protein glycosylation and lifespan extension by metformin. Competitive-aging screening coupled to multiple-regression modeling provides a powerful, straight-forward way to identify aging factors in yeast and their interactions with pharmacological interventions.

genetics↗

bioRxiv2018

An interaction map of transcription factors controlling gynoecium development in Arabidopsis

Flowers are composed of different organs, whose identity is defined at the molecular by the combinatorial activity of transcription factors (TFs). MADS-box TFs interact forming complexes that have been schematized in the quartet model. The gynoecium is the female reproductive part in the flower, crucial for plant reproduction, and fruit and seed production. Once carpel identity is established, a gynoecium containing many tissues arises. Several TFs have been identified as regulators of gynoecium development, and some of these TFs form complexes. However, broad knowledge about the interactions among these TFs is still scarce. In this work, we used a systems biology approach to understand the formation of a complex reproductive unit as the gynoecium by mapping binary interactions between well-characterized TFs. We analyzed over 3500 combinations and detected more than 200 protein-protein interactions (PPIs), resulting in a process specific interaction map. Topological analyses suggest hidden functions and novel roles for many TFs. Furthermore, a relationship between TFs involved in auxin and cytokinin signaling pathways and other TFs was observed. We analyzed the network by combining PPI data, expression and genetic data, allowing us to dissect it into several dynamic spatio-temporal sub-networks related to gynoecium development subprocesses.

plant biology↗

bioRxiv2017

Protein Moonlighting Revealed by Non-Catalytic Phenotypes of Yeast Enzymes

A single gene can partake in several biological processes, and therefore gene deletions can lead to different--sometimes unexpected--phenotypes. However, it is not always clear whether such pleiotropy reflects the loss of a unique molecular activity involved in different processes or the loss of a multifunctional protein. Here, using Saccharomyces cerevisiae metabolism as a model, we systematically test the null hypothesis that enzyme phenotypes depend on a single annotated molecular function, namely their catalysis. We screened a set of carefully selected genes by quantifying the contribution of catalysis to gene-deletion phenotypes under different environmental conditions. While most phenotypes were explained by loss of catalysis, 30% could be readily complemented by a catalytically-inactive enzyme. Such non-catalytic phenotypes were frequent in the Alt1 and Bat2 transaminases and in the isoleucine/valine-biosynthetic enzymes Ilv1 and Ilv2, suggesting novel \"moonlighting\" activities in these proteins. Furthermore, differential genetic-interaction profiles of gene-deletion and catalytic mutants indicated that ILV1 is functionally associated to regulatory processes, specifically to chromatin modification. Our systematic study shows that gene-loss phenotypes and their genetic interactions are frequently not driven by the loss of an annotated catalytic function, underscoring the moonlighting nature of cellular metabolism.

genetics↗

bioRxiv2017

Genome-Wide Mechanisms of Lifespan Extension by Dietary Restriction in Yeast

Dietary restriction is arguably the most promising non-pharmacological intervention to extend human life and health span. Yet, only few genetic regulators mediating the cellular response to dietary restriction are known, and the question remains which other transcription factors and regulatory pathways are involved. To gain a comprehensive view of how lifespan extension under dietary restriction is elicited, we screened the chronological lifespan of most gene deletions of Saccharomyces cerevisiae under two dietary regimens, restricted and non-restricted. We identified 472 mutants with enhanced or diminished extension of lifespan by dietary restriction. Functional analysis of such dietary-restriction genes revealed novel processes underlying longevity specifically by dietary restriction. Importantly, this set of genes allowed us to generate a prioritized catalogue of transcription factors orchestrating the dietary-restriction response, which underscored the relevance of cell-cycle arrest control as a key mechanism of chronological longevity in yeast. We show that the transcription factor Ste12 is needed for full lifespan extension and cell-cycle arrest in response to nutrient limitation; linking the pheromone/invasive growth pathway with cell survivorship. Strikingly, STE12 overexpression was sufficient to extend chronological lifespan under non-restricted conditions. Our global picture of the genetic players of longevity by dietary restriction highlights intricate regulatory cross-talks in aging cells.

genetics↗