Biology subjects

Espinosa-Cantu, A.

Publications and source records attributed to Espinosa-Cantu, A..

4 recordsLinked to original sources

bioRxiv2026

A competition-protection balance explains the evolution of resistance within simple microbial communities

Stressful environments can pose a threat to microbial populations, but resistant individuals can emerge and avoid extinction. Adaptation to stress is classically studied in isolated microbial species, ignoring ecological interactions, a key component of natural ecosystems. A growing body of experimental work has shown that community context can affect resistance evolution due to a large variety of mechanisms. Here we set out to identify the minimal components needed to predict the likelihood of acquiring resistance in a focal species embedded within a simple community. To achieve this, we developed a mathematical model based on evolutionary rescue theory and validated it with two experimental systems: Escherichia coli evolving on exposure to the antibiotic nitrofurantoin alone or with one of 14 bacterial isolates from urinary tract infections, and Microbacterium liquefaciens evolving in ampicillin alone or with ampicillin-degrading Comamonas testosteroni. One key factor that emerged from our analyses - the relative strength of competition versus protection - could explain whether a focal species is more or less likely to evolve resistance in the presence of a partner species. While competition always hinders the emergence of resistance, protection can rescue the focal species in two ways: (i) ecological rescue, when the partner species completely removes the antibiotic and favors the survival of the susceptible population, or (ii) evolutionary rescue, when the partner only lowers antibiotic concentrations and favors the emergence of resistant variants, a previously overlooked evolutionary consequence of detoxification. Overall, by integrating theory and experiments, we propose a framework that clarifies how ecological interactions favor or hinder the evolution of resistance to antibiotics or potentially other stressors. SignificanceBacteria can rapidly adapt to resist stressors, such as antibiotics. While resistance evolution in single populations or species is well understood, it remains unclear how ecological interactions with other species influence this process. We develop a mathematical framework to predict what interactions should favor resistance evolution and validate it with two sets of experiments where bacteria adapt to antibiotics in small communities. Our work demonstrates that interactions with other species shape the probability of evolving resistance in a predictable way, determined by the balance between competition and protection against the stressor. By identifying the key factors that drive these dynamics, our work helps explain how bacteria adapt to environmental challenges within species-rich ecosystems.

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↗

bioRxiv2021

Ribosomal intron-mediated switch governs yeast survival in starvation

Introns are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein (RP) genes differing primarily in their introns2-4. Despite recent findings on the role of RP introns under stress and starvation5-7, understanding the contribution of introns to ribosome regulation remains challenging. Here, combining isogrowth profiling8 with single-cell protein measurements9, we found that introns can mediate inducible phenotypic heterogeneity conferring a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, mediated by an intron in the 5 untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low Rps22B protein levels resulted in prolonged survival under sustained starvation, while high Rps22B levels enabled cells to grow faster after transient starvation. Further, yeast growing at high sugar concentrations - similar to those in ripe grapes - exhibit bimodal Rps22B expression when approaching stationary phase. Differential intron-mediated regulation of RP genes thus provides a way to diversify the population when starvation looms in natural environments. Our findings reveal a new role for introns in inducing phenotypic heterogeneity in changing environments and suggest that duplicated RP genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness10.

systems 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↗