Biology subjects

Sokolowska, E.

Publications and source records attributed to Sokolowska, E..

4 recordsLinked to original sources

bioRxiv2025

Identification of dehydrin protein complexes in vivo reveals functional interactions of LEA5 with OSCA3, PIP2B and PLDα1 in plant water-deficit stress

Climate change and especially the concomitant increasing frequency of drought and salinity induced water-deficit stresses, is a major limiting factor of plant growth and crop productivity worldwide. Understanding the adaptive responses of plants to water-deficit stress has therefore become a central challenge in plant biotechnology. Considerable evidence indicates that late embryogenesis abundant (LEA) proteins contribute to water-deficit stress tolerance and the stabilization of metabolic enzymes, yet the molecular basis of these responses remains unknown. To date, limited direct evidence for specific in vivo interactions between LEA proteins and their molecular targets has been reported. Here, we identify for the first time the native in vivo interactome of three Arabidopsis dehydrin LEA proteins - LEA4 (COR47), LEA5 (ERD10), and LEA10 (ERD14) - expressed under their own promoters and in response to salt stress. Our results show that LEA4, LEA5, and LEA10 dehydrins interact with each other, and share six common candidate protein interactors, suggesting that they form a core protein complex in salt stress conditions. We confirmed the direct protein-protein interaction between LEA5 with LEA4, LEA10, OSCA3, PLD1, PIP2B and OST1/AHA1 at the biochemical level. Phenotypic analyses of loss-of-function genetic mutants revealed that the interactions of LEA5 with OSCA3 and PIP2B promote seed germination under salt stress. LEA5 interaction with PLD1 promotes root growth under salt stress, while its interaction with PIP2B enhances root growth under osmotic stress, indicating distinct stress-specific functional roles for each interaction. In conclusion, this study identifies the native in vivo interactions of three dehydrin proteins, while uncovering the functional relevance of these interactions under salt and osmotic stress conditions, thus providing novel mechanistic insights into the role of LEA proteins in water-deficit stress adaptation.

plant biology↗

bioRxiv2023

Characterization of tomato canal-1 mutant using a multi-omics approach

The recently described canal-1 tomato mutant, which has a variegated leaf phenotype, has been shown to affect canalization of yield. The corresponding protein is orthologous to AtSCO2 - SNOWY COTYLEDON2, which has suggested roles in thylakoid biogenesis. Here we characterize the canal-1 mutant through a multi-omics approach, by comparing mutant to wild-type tissues. While white canal-1 leaves are devoid of chlorophyll, green leaves of the mutant appear wild-type-like, despite an impaired protein function. Transcriptomic data suggest that green mutant leaves compensate for this impaired protein function by upregulation of transcription of photosystem assembly and photosystem component genes, thereby allowing adequate photosystem establishment, which is reflected in their wild-type-like proteome. White canal-1 leaves, however, likely fail to reach a certain threshold enabling this overcompensation, and plastids get trapped in an undeveloped state, while additionally suffering from high light stress, indicated by the overexpression of ELIP homolog genes. The metabolic profile of white and to a lesser degree also green tissues revealed upregulation of amino acid levels, that was at least partially mediated by transcriptional and proteomic upregulation. These combined changes are indicative of a stress response and suggest that white tissues behave as carbon sinks. In summary, our work demonstrates the relevance of the SCO2 protein in both photosystem assembly and as a consequence in the canalization of yield. Significance statementThe variegated canalized-1 tomato mutant was recently described and the underlying gene SCO2 suggested to be a yield canalization gene. Through a multi-omics approach we show that mutants require a transcriptional upregulation of photosystem components and assembly components, likely as overcompensation for partially impaired SCO2 function, to produce a wild type-like proteome and functional photosynthetic tissue Our data, furthermore, suggest that variation of green to white leaf area from plant to plant leads to the yield variation.

plant biology↗

bioRxiv2021

Identification and Functional Annotation of Long Intergenic Non-coding RNAs in the Brassicaceae

Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts with critical biological functions. Despite the wealth of RNA-seq data available, lincRNA identification lags in the plant lineage. In addition, there is a need for a harmonized identification and annotation effort to enable cross-species functional and genomic comparisons. In this study we processed >24 Tbp of RNA-seq data from >16,000 experiments to identify ~130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used Nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify functional motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our dataset with sequence or transcriptional evolutionary conservation, including lincRNAs transcribed adjacent to orthologous genes that display little sequence similarity and likely function as transcriptional regulators. Finally, we used guilt-by-association techniques to further classify these lincRNAs according to putative function. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, short ORFs, and whose expression is modulated by abiotic stress are a few of the annotations that will prioritize and guide future functional analyses.

genomics↗

bioRxiv2018

Genome-wide Association Study of Anxiety and Stress-related Disorders in the iPSYCH Cohort

Anxiety and stress-related disorders (ASRD) are among the most common mental disorders with the majority of patients suffering from additional disorders. Family and twin studies indicate that genetic and environmental factors are underlying their etiology. As ASRD are likely to configure various expressions of abnormalities in the basic stress-response system, we conducted a genome-wide association study including 12,655 cases with various anxiety and stress-related diagnoses and 19,225 controls. Standard association analyses were performed supplemented by a framework of sensitivity analyses. Variants in PDE4B showed consistent association with ASRD across a wide range of our analyses. In mice models, alternations in PDE4B expression were observed in those mice displaying anxious behavior after exposure to chronic stress. We also showed that 28% of the variance in ASRD was accounted for by common variants and that the genetic signature of ASRD overlapped with psychiatric traits, educational outcomes, obesity-related phenotypes, smoking, and reproductive success.

genetics↗