Biology subjects

Sorokin, Y.

Publications and source records attributed to Sorokin, Y..

4 recordsLinked to original sources

bioRxiv2024

Reversion to metabolic autonomy underpins evolutionary rescue of a bacterial obligate mutualism

Populations facing lethal environmental change can avoid extinction by undergoing rapid genetic adaptation, a phenomenon termed evolutionary rescue. While this phenomenon has been the focus of much theoretical and empirical research, our understanding of evolutionary rescue in communities consisting of interacting species is still limited, especially in mutualistic communities, where evolutionary rescue is expected to be constrained by the less adaptable partner. Here, we explored empirically the likelihood, population dynamics, and genetic mechanisms underpinning evolutionary rescue in an obligate mutualism in which auxotrophic Escherichia coli strains exchanged essential amino acids reciprocally. We observed that >80% of the communities avoided extinction when exposed to two different types of lethal and abrupt stresses. Of note, only one of the strains survived in all cases. Genetic and phenotypic analyses show that this strain reverted to autonomy by metabolically bypassing the auxotrophy, but we found little evidence of specific adaptation to the stressors. Crucially, we found that the mutualistic partners were substantially more sensitive to both stresses than prototrophs, so that reversion to autonomy was sufficient to alleviate stress below lethal levels. We observed that increased sensitivity was common across several other stresses, suggesting that this may be a general property of obligate mutualisms mediated by amino acid exchange. Our results reveal that evolutionary rescue may depend critically on the specific genetic and physiological details of the interacting partners, adding rich layers of complexity to the endeavor of predicting the fate of microbial communities facing intense environmental deterioration.

evolutionary biology↗

bioRxiv2023

Evolution in microbial microcosms is highly parallel regardless of the presence of interacting species

During laboratory evolution, replicate bacterial populations often follow similar trajectories, thus their evolution is potentially predictable. However, predicting the evolution of natural populations, which are commonly embedded in multispecies communities, would prove extremely difficult if adaptations are contingent on the identity of the interacting species. The extent to which adaptations typically depend on coevolving partners remains poorly understood, since coevolution is commonly studied using small-scale experiments involving few species, making it challenging to extract general trends. To address this knowledge gap, we study the adaptations that occurred in strains of each of 11 species that were either evolved in monoculture or in multiple pairwise co-cultures. While we detect slight but significant partner-specific effects we find that the majority of evolutionary changes that occur are robust across strains that evolved with different partners; species growth abilities increase by a similar factor regardless of partners identity, shifts in community compositions and interactions are similar between pairs of coevolved and separately evolved strains, and the majority of parallelly mutated genes were detected in multiple biotic conditions. We hypothesized that these results might arise from the fact that ancestral strains are maladapted to the abiotic environment, thus having a pool of adaptations that are beneficial regardless of the biotic partners. Therefore, we conducted a second experiment with strains that were pre-adapted to the abiotic conditions before being co-cultured. We find that even after [~]400 generations of pre-adaptation, evolution is surprisingly non-partner-specific. Further work is required in order to elucidate the factors that influence partner-specificity of coevolution, but our results suggest that selection imposed by the biotic environment may play a secondary role to that imposed by abiotic conditions, making predictions regarding coevolutionary dynamics less challenging than previously thought.

evolutionary biology↗

bioRxiv2020

Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales

Managing and engineering microbial communities relies on the ability to predict their composition. While progress has been made on predicting compositions on short, ecological timescales, there is still little work aimed at predicting compositions on evolutionary timescales. Therefore, it is still unknown for how long communities typically remain stable after reaching ecological equilibrium, and how repeatable and predictable are changes when they occur. Here, we address this knowledge gap by tracking the composition of 87 two- and three-species bacterial communities for ~400 generations. We find that community composition typically changed during evolution, but that the composition of replicate communities remained similar. Furthermore, these changes were predictable in a bottom-up approach - changes in the composition of trios were consistent with those that occurred in pairs during coevolution. Our results demonstrate that simple assembly rules can hold even on evolutionary timescales, suggesting it may be possible to forecast the evolution of microbial communities.

microbiology↗

bioRxiv2018

Interpreting coronary artery disease risk through gene-environment interactions in gene regulation

GWAS and eQTL studies identified thousands of genetic variants associated with complex traits and gene expression. Despite the important role of environmental exposures in complex traits, only a limited number of environmental factors are measured in these studies. Measuring molecular phenotypes in tightly controlled cellular environments provides a more tractable setting to study gene-environment interactions in the absence of other confounding variables.\n\nWe performed RNA-seq and ATAC-seq in endothelial cells exposed to retinoic acid, dexamethasone, caffeine, and selenium to model genetic and environmental effects on gene regulation in the vascular endothelium, a common site of pathology in cardiovascular disease. We found that genes near regions of differentially accessible chromatin were more likely to be differentially expressed (OR = [3.41, 6.52], p < 10-16). Furthermore, we confirmed that environment-specific changes in transcription factor binding are a key mechanism for cellular response to environmental stimuli. SNPs in these transcription response factor footprints for dexamethasone, caffeine, and retinoic acid were enriched in GTEx eQTLs from artery tissues indicating that these environmental conditions are latently present in GTEx samples. Additionally, SNPs in footprints for response factors in caffeine are enriched in colocalized eQTLs for coronary artery disease (CAD), suggesting a role for caffeine in CAD risk. Interestingly, each treatment may amplify or buffer genetic risk for CAD, depending on the particular SNP considered.

genomics↗