Biology subjects

Koska, S.

Publications and source records attributed to Koska, S..

9 recordsLinked to original sources

bioRxiv2025

Evolutionary expression patterns in developing biofilms of uropathogenic Escherichia coli reveal embryo-like features

Developing biofilms of the gram-positive, soil-dwelling bacterium Bacillus subtilis exhibit expression patterns and evolutionary imprints similar to those observed in eukaryotic embryos. However, the universality of these evolutionary and developmental regularities has not yet been explored in other biofilm-forming bacteria, including pathogens. To broaden the perspective on ontogeny-phylogeny correlations in bacteria, we recovered phylotranscriptomic and phyloproteomic trajectories throughout the entire biofilm development of uropathogenic Escherichia coli UTI89. Here, we show that biofilm growth in E. coli UTI89 positively correlates with the evolutionary age of expressed genes, with developing biofilms progressively expressing younger and more divergent genes. These findings suggest that biofilm formation in gram-negative bacteria is not macroevolutionarily naive and that evolutionary imprints are a pervasive feature of bacterial biofilm development. While these regularities apply to the developmental expression patterns of bulk biofilms, the question remains whether evolutionary stratification occurs within the spatial regions of individual biofilms. To address this, we analyzed expression profiles across concentric regions of E. coli UTI89 biofilms at three developmental stages. This analysis revealed that gene expression, functional patterns, and evolutionary imprints are influenced by both developmental timing and distance from the biofilm center. Together, these findings demonstrate that the growth of uropathogenic E. coli biofilms is governed by both temporal and spatial macroevolutionary logic, drawing intriguing parallels to organismal development in multicellular eukaryotic lineages.

evolutionary biology↗

bioRxiv2024

Evolutionary trends in the emergence of skeletal cell types.

The emergence of novel cell types fuels evolutionary innovations and contributes to the diversity of life forms and their morphological and functional traits. Cell types are fundamental functional units of multicellular organisms defined by their specific gene expression programs. The evolution of these transcriptional programs is driven by genetic changes, such as gene co-option and cis- regulatory evolution, known to facilitate the assembly or rewiring of molecular networks and give rise to new cell types with specialized functions. However, the role of novel genes in this complex evolutionary process is underexplored. Here, we examine the trends in skeletal cell type evolution with a focus on lineage-specific genes. We find that immature chondrocytes express the oldest transcriptome and resemble ancestral skeletogenic cell type, supporting the existence of a conserved genetic program for cartilage development in bilaterians. The subsequent acquisition of lineage-restricted genes led to the individuation of the ancient gene expression program and powered the emergence of osteoblasts and hypertrophic chondrocytes. We found a significant enrichment of Vertebrate-specific genes in osteoblasts and Gnathostome-specific genes in hypertrophic chondrocytes. By identifying the functional properties of the recruited genes, coupled with the recently discovered fossil evidence, our findings challenge the long-standing view on the evolution of vertebrate skeletal structures and suggest that endochondral ossification and chondrocyte hypertrophy evolved already in the last common ancestors of gnathostomes. Finally, our findings highlight the critical role of novel genes in shaping cellular diversity.

evolutionary biology↗

bioRxiv2024

Identification of small molecule enhancers of NK cell tumoricidal activity via a tumor microenvironment-mimicking co-culture assay

The tumor microenvironment (TME) is a pro-cancerous niche harboring immunosuppressive factors that are secreted by cancer cells and the surrounding cancer-supportive tissue, such as kynurenine, prostaglandin E2 and transforming growth factor {beta} (TGF{beta}). These factors dampen the activity of cytotoxic lymphocytes like natural killer (NK) cells, allowing evasion of immune cell-mediated killing. To identify small molecules that counteract the immunosuppressive effect of the TME and restore NK cell-mediated cytotoxicity, we developed a phenotypic co-culture assay of cancer cells and primary lymphocytes suitable for medium-throughput screening. We discovered small molecules that restore NK cell-mediated cytotoxicity through diverse mechanisms. The potent TGF{beta} type I receptor (TGF{beta}R-1) inhibitor, RepSox, stood out as superior to other TGF{beta}R-1 inhibitors due to its ability to abolish the effects of both inhibitory factors used in our setup. This mode of action goes beyond TGF{beta}R-1 inhibition and is related to the simultaneous abrogation of cyclooxygenase 1 (COX1) activity.

immunology↗

bioRxiv2024

Somatic embryogenesis of grapevine (Vitis vinifera) expresses a transcriptomic hourglass

At the molecular level, multicellular eukaryotic lineages and bacterial biofilms show predictable evolutionary footprints in their development. For instance, the zygotic embryogenesis of Arabidopsis, which is initiated by gamete fusion, shows hourglass-shaped ontogeny-phylogeny correlations at the transcriptome level. However, many plants are capable of yielding a fully viable next generation by somatic embryogenesis -- a comparable developmental process that usually starts by the embryogenic induction of a diploid somatic cell. This leads to the question: is the hourglass-shaped ontogeny-phylogeny correlation preserved in somatic embryogenesis? To explore the correspondence between ontogeny and phylogeny in this alternative developmental route in plants, we developed a new and highly efficient model of somatic embryogenesis in grapevine (Vitis vinifera) and sequenced its developmental transcriptomes. By combining the evolutionary properties of grapevine genes with their expression values, which were recovered from early induction until the formation of juvenile plants, we found a strongly supported hourglass-shaped developmental trajectory. However, in contrast to zygotic embryogenesis in Arabidopsis where the torpedo stage was evolutionary the most inert, we found that in the somatic embryogenesis of grapevine the heart stage expressed evolutionary the oldest and the most conserved transcriptome. This is a surprising finding because it suggests a better evolutionary system-level analogy between animal development and plant somatic embryogenesis than zygotic embryogenesis. We conclude that macroevolutionary logic is deeply hardwired in plant ontogeny and that somatic embryogenesis is likely a primordial embryogenic program in plants.

evolutionary biology↗

bioRxiv2023

Detection of a Mitochondrial Stress Phenotype using the Cell Painting Assay

Mitochondria are cellular powerhouses and crucial for cell function. However, these organelles are vulnerable to internal and external perturbagens that may impair mitochondrial function and eventually lead to cell death. In particular, small molecules may impact mitochondrial function and cardio- or hepatotoxicity caused by numerous drugs links mitochondrial toxicity to these adverse effects. Therefore, the influence of small molecules on mitochondrial homeostasis is at best assessed early on in the characterization of biologically active small molecules and drug discovery. We demonstrate that unbiased morphological profiling by means of the Cell Painting assay (CPA) can detect mitochondrial stress coupled to the induction of integrated stress response. This activity is common for compounds addressing different targets, is not shared by direct inhibitors of the electron transport chain and enables prediction of mitochondrial stress induction for small molecules that are profiled using CPA.

cell biology↗

bioRxiv2023

Illuminating Dark Chemical Matter using the Cell Painting Assay

The identification of bioactive small molecules is at the heart of chemical biology and medicinal research. The screening for modulators of disease-relevant targets and phenotypes is the first step on the way to new drugs. Therefore, large compound libraries have been synthesized and employed by academia and, particularly, pharmaceutical companies to meet the need for chemical entities that are as diverse as possible. Extensive screening of these compound libraries revealed a portion of small molecules that is inactive in more than 100 different assays and was therefore termed dark chemical matter (DCM). Deorphanization of DCM promises to yield very selective compounds as they, by definition, should have less off-target effects. We employed morphological profiling using the Cell painting assay (CPA) to detect bioactive DCM compounds. CPA is not biased to a given target or phenotype and can detect various unrelated mechanisms and modes of action. Within the DCM collection, we identified bioactive compounds and confirmed several modulators of microtubules, DNA synthesis and pyrimidine biosynthesis. Profiling approaches are therefore powerful tools to probe compound collections for bioactivity in an unbiased manner and particularly suitable for deorphanization of DCM.

cell biology↗

bioRxiv2022

Targeting oncogenic KRasG13C with nucleotide-based covalent inhibitors

Mutations within Ras proteins represent major drivers in human cancer. In this study, we report the structure-based design, synthesis, as well as biochemical and cellular evaluation of nucleotide-based covalent inhibitors for KRasG13C, an important oncogenic mutant of Ras that has not been successfully addressed in the past. Mass spectrometry experiments and kinetic studies reveal promising molecular properties of these covalent inhibitors, and X-ray crystallographic analysis has yielded the first reported crystal structures of KRasG13C covalently locked with these GDP analogues. Importantly, KRasG13C covalently modified with these inhibitors can no longer undergo SOS-catalysed nucleotide exchange. As a final proof-of-concept, we show that in contrast to KRasG13C, the covalently locked protein is unable to induce oncogenic signalling in cells, further highlighting the possibility of using nucleotide-based inhibitors with covalent warheads in KRasG13C-driven cancer.

cancer biology↗

bioRxiv2022

A novel time-lapse imaging method for studying developing bacterial biofilms

In nature, bacteria prevailingly reside in the form of biofilms. These elaborately organized surface-bound assemblages of bacterial cells show numerous features of multicellular organization. We recently showed that biofilm growth is a true developmental process, which resembles developmental processes in multicellular eukaryotes. To study the biofilm growth, in a fashion of eukaryotic ontogeny, it is essential to define dynamics and critical transitional phases of this process. The first step in this endeavor is to record the gross morphological changes of biofilm ontogeny under standardized conditions. This visual information is instrumental in guiding the sampling strategy for the later omics analyses of biofilm ontogeny. However, none of the currently available visualizations methods is specifically tailored for recording gross morphology across the whole biofilm development. To address this void, here we present an affordable Arduino-based approach for time-lapse visualization of complete biofilm ontogeny. The major challenge in recording biofilm development on the air-solid interphase is water condensation, which compromises filming directly through the lid of a Petri dish. To overcome these trade-offs, we developed an Arduino microcontroller setup which synchronizes a robotic arm, responsible for opening and closing the Petri dish lid, with the activity of a stereomicroscope-mounted camera and lighting conditions. We placed this setup into microbiological incubator that maintains temperature and humidity during the biofilm growth. As a proof-of-principle, we recorded biofilm development of five Bacillus subtilis strains that show different morphological and developmental dynamics.

microbiology↗

bioRxiv2020

Embryo-like features in developing Bacillus subtilis biofilms

Correspondence between evolution and development has been discussed for more than two centuries1. Recent work reveals that phylogeny-ontogeny correlations are indeed present in developmental transcriptomes of eukaryotic clades with complex multicellularity2-10. Nevertheless, it has been largely ignored that the pervasive presence of phylogeny-ontogeny correlations is a hallmark of development in eukaryotes6, 10-12. This perspective opens a possibility to look for similar parallelisms in biological settings where developmental logic and multicellular complexity are more obscure13-16. For instance, it has been increasingly recognized that multicellular behaviour underlies biofilm formation in bacteria13, 14, 17-19. However, it remains unclear whether bacterial biofilm growth shares some basic principles with development in complex eukaryotes14-16, 18, 20. Here we show that the ontogeny of growing Bacillus subtilis biofilms recapitulates phylogeny at the expression level. Using time-resolved transcriptome and proteome profiles, we found that biofilm ontogeny correlates with the evolutionary measures, in a way that evolutionary younger and more diverged genes were increasingly expressed towards later timepoints of biofilm growth. Molecular and morphological signatures also revealed that biofilm growth is highly regulated and organized into discrete ontogenetic stages, analogous to those of eukaryotic embryos11, 21. Together, this suggests that biofilm formation in Bacillus is a bona fide developmental process comparable to organismal development in animals, plants and fungi. Given that most cells on Earth reside in the form of biofilms22 and that biofilms represent the oldest known fossils23, we anticipate that the widely-adopted vision of the first life as a single-cell and free-living organism needs rethinking.

evolutionary biology↗