Biology subjects

Potapenko, E. V.

Publications and source records attributed to Potapenko, E. V..

4 recordsLinked to original sources

bioRxiv2025

Genome size variation is attributed to adaptive purging of transposable elements

A substantial variation in genome size has been observed among individuals of the same species. Theory predicts that increased genome size may confer an advantage in populations with small effective size. However, contradictory evidence for the correlation with environmental variation, and limited understanding of the underlying genetic mechanisms, has cast doubts on the adaptive role of genome size variation. To address this, we studied two Hordeum species which were collected at the same sites along a wide range of environments but different in life habit (annual/perrenial) and mating strategy (self/out-crossing). We observed significant variation in genome size, with differences of up to 10% consistently detected in both species. Mating system influenced only the proportion of variation maintained within populations but not the overall range of genome size. In both species, drought emerged as the primary environmental factor associated with genome expansion, with transposable elements (TE) accumulation identified as the main driver of this expansion. Genome-wide association studies revealed that TE silencing is the key mechanism regulating genome size, and that selection favors smaller genomes among individuals growing at suitable habitats. Under increasingly stressful conditions, the regulation of TE activity fades, leading to TE accumulation and genome expansion, thereby increasing genetic variation available for selection. This integrative study provides a comprehensive view of how genome size is regulated in natural populations and highlights its exaptive role in inducing genetic variation under environmental stress.

evolutionary biology↗

bioRxiv2025

Pcbp1 orchestrates amino acid metabolism burst during the naive-to-primed pluripotency transition

Embryo implantation is accompanied by the naive-to-primed pluripotency transition in epiblast cells, making them receptive to external differentiation signals. In addition to this developmental program switch, implantation suggests that an anabolic boost is required for this process, as the embryo-uterine connection begins supplying the requisite nutrients. In this study, we show that the DNA-binding protein Pcbp1 plays a key role in intensifying amino acid metabolism during the priming of pluripotent stem cells. Knockout of the Pcbp1 gene leads to embryo growth arrest a few days after implantation. By modeling the naive-to-primed pluripotency transition in vitro, we observe reduced proliferation and induction of apoptosis in cells deficient for Pcbp1. Using multi-omics approaches, we uncover a crucial role for Pcbp1 in driving a transcriptional burst of numerous genes involved in the import and the de novo synthesis of essential and conditionally essential amino acids. Pcbp1 deficiency is consequently associated with a slowdown in protein biosynthesis, explaining the early lethal phenotype of knockout embryos. Our findings thus uncover the molecular mechanisms underlying anabolic changes during the naive-to-primed pluripotency transition and highlight the essential role of Pcbp1 in this process, also pointing to its functions in highly proliferative cells. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/658314v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@1e17b48org.highwire.dtl.DTLVardef@64e940org.highwire.dtl.DTLVardef@10d6b00org.highwire.dtl.DTLVardef@1ec0d23_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2024

Transposable elements are entangled in rapid adaptation to climate change

Biodiversity conservation is urged at biodiversity hotspots that are under constant threat from anthropogenic development, yet a careful examination of the adaptive potential is a prerequisite for action. The Levant is considered a biodiversity hotspot and the distribution edge for many species, including important crop wild relatives. This region is under accelerated desertification and constantly disturbed by human activities, thus urging intervenient action. We collected and sequenced 300 wild barley plants along an eco-geographic gradient following a unique ecological-genetic sampling design. This scheme enabled to overcome the tight correlation between environmental and geographic distances. Phenotypic data was collected from 3600 progeny plants over three years and enabled to identify adaptive haplotype blocks comprised of phenological regulating genes tightly linked to drought and heat responsive genes. These haplotype blocks were highly enriched for transposable elements insertions, likely regulating genetic variation around adaptive genes, especially in stressed populations. Ecological and evolutionary models using over 2600 observations were combined to predict maladaptive risk, indicating that populations will be funneled into higher water availability refugia habitats while increasing isolation. Our findings highlight the main factors affecting rapid local adaptation and provide important recommendations for biodiversity management and conservation.

plant biology↗

bioRxiv2023

Newly obtained genome of fungi-related amoeba is enriched with genes shared with animals-related protists

Nuclearariids are a group of Opisthokonta, forming the deepest branch in Holomycota - one of the two major Opisthokonta clades, containing Fungi as a crawn group. They are the only members of Holomycota retaining the filose amoeboid state ancestral for Opisthokonta. The newly assembled genome of Nuclearia thermophila (Holomycota, Rotosphaerida) had a total length of 49 Mb, 15 321 protein-coding genes and a GC percentage of 44%. This is the first sequenced genome for this genus and the the third for Rotosphaerida as a whole. It was shown that N. thermophila shares more protein domains with Holozoa, than with the rest of Holomycota. Protein domains that were presumably acquired or lost by the common ancestors of the Holomycota and Holozoa groups were identified. The Holomycota ancestor had probably more gains and losses of protein domains compared to the Holozoa ancestor, which is particularly true for metabolism-related domains. However, this trend should be confirmed by studying the genomes of free-living organisms of the Teretosporea group.

genomics↗