Biology subjects

Sokolskyi, T.

Publications and source records attributed to Sokolskyi, T..

5 recordsLinked to original sources

bioRxiv2026

Simple case of prebiotic evolution: vesicle populations can respond to selection for greater turbidity via emergent cooperative dynamics

Adaptive evolution has long been hypothesized to be possible in the absence of genetic molecules, but experimental evidence remains lacking. Fatty acid vesicles represent an intriguing model to study the emergence of prebiotic evolution, since they can spontaneously grow and divide and have been hypothesized to be capable of non-genetic inheritance. In this study we conducted multiple experiments to test whether vesicle populations can respond to artificial selection for greater turbidity and, if so, whether that response can be tied to an inheritance-like mechanism. We prepared 96 independent vesicle populations, incubated them for 24 hours and then selected half the populations to propagate into the next generation. The populations to propagate were picked either randomly, representing drift controls, or were the populations with the greatest turbidity, representing selection. Population propagation involved resuspension, transfer into fresh buffer, feeding with an amphiphile stock, and then incubating for the next 24 hours. In three replicate experiments run for at least 10 generations, we observed consistently greater turbidity in selection lineages compared to drift, as well as a reduction in the heritability (i.e., the correlation between parent and offspring turbidities). We conducted additional experiments to evaluate whether this response to selection is caused by a simple carryover effect or reflects cooperative dynamics, where vesicles from the parental generation affect newly formed vesicles in the offspring generation. The response to selection is much lower if we omitted the resuspension step and/or if we did not feed transfers with amphiphiles but instead mixed them we pre-formed vesicles. Combined with imaging and other analyses of the resuspension and feeding process, these results suggest that cooperative vesicle dynamics occur, where a small number of intact vesicles from a parental generation alters the dynamics of new vesicle formation following food addition. Overall, this study represents the first experimental finding of a response to artificial selection in prebiotic chemistry.

evolutionary biology↗

bioRxiv2024

Measuring heritability in messy prebiotic chemical systems

A key question in origins-of-life research, is whether heritability, and thus evolution, could have preceded genes. Out-of-equilibrium chemical reaction networks with multiple autocatalytic motifs may provide chemical "memory" and serve as units of heritability, but experimental validation is lacking. We established conditions that may be conducive to the emergence of heritable variation and developed methods to search for heritability and autocatalysis. We prepared a food set (FS) of three organic species, three inorganic salts and pyrite. We conducted a serial dilution experiment where FS was incubated for 24 hours, after which a 20% fraction was transferred into freshly prepared FS that went through the same procedure, repeated for 10 generations. To serve as controls, we also incubated the fresh solutions in each generation. We compared the chemical composition of transfer vials and no-transfer controls using liquid chromatography-mass spectrometry (LCMS), with metrics adapted from ecology and evolutionary biology. While variability was high, focusing on a subset of chemicals with more consistent patterns revealed evidence of heritable variation among vials. Using rule-based chemical reaction network inference, constrained by the LCMS data, we identified a plausible FS-driven chemical reaction network that was found to contain numerous autocatalytic cycles.

evolutionary biology↗

bioRxiv2022

Role of horizontal gene transfers and microbial ecology in the evolution of fluxes through the tricarboxylic acid cycle

The origin of carbon fixation is a fundamental question in astrobiology. While the Calvin cycle is the most active on the modern Earth, the reductive TCA cycle (rTCA) pathway for carbon fixation has been proposed to have played an important role in early evolution. In this study, we examined the evolution of key enzymes in the rTCA, which are rare in extant organisms, occurring in a few groups of Bacteria and Archaea. We investigated one of the least common reactions of this pathway, cleavage of citrate into oxaloacetate and acetyl-CoA, which can be performed by either a two-enzyme system (CCS/CCL) or a single enzyme (ACL) that is assumed to be the result of fusion of the two active sites into a single polypeptide. For broader context, we also studied functionally diverged homologs of these enzymes, succinyl-CoA synthetase (SCS) and citrate synthase (CS). Our phylogenetic analysis of these enzymes in Bacteria and Archaea shows that SCS, a homolog of CCS from distant bacterial taxa capable of citrate cleavage, are monophyletic, suggesting linked horizontal gene transfers of SCS and citrate cleavage enzymes. We also found evidence of the horizontal transfer of SCS from a clade of anaerobic Archaea (Archaeoglobi, Methanomicrobia or Crenarchaeota) to an ancestor of Cyanobacteria/Melainabacteria clade - both of whom share a succinate semialdehyde shunt in their oxidative TCA cycles. We also identified new bacterial and archaeal taxa for which complete rTCA cycles are theoretically possible, including Syntrophobacter, Desulfofundulus, Beggiatoa, Caldithrix, Ca. Acidulodesulfobacterales and Ca. Micrarachaeota. Finally, we suggest a possibility for syntrophically-regulated fluxes through oxidative and reductive TCA reactions in microbial communities particularly Haloarchaea-Nanohaloarchaea symbiosis and its implications for the Purple Earth hypothesis. We discuss how the inclusion of an ecological perspective in the studies of evolution of ancient metabolic pathways may be beneficial to understand origins of life.

evolutionary biology↗

bioRxiv2022

Resistance of mitochondrial DNA to chemical-induced germline mutations is independent of mitophagy in C. elegans

Mitochondrial DNA (mtDNA) is prone to mutation in aging and over evolutionary time, yet the processes that regulate the accumulation of de novo mtDNA mutations and modulate mtDNA heteroplasmy are not fully elucidated. Mitochondria lack certain DNA repair processes, which could contribute to polymerase error-induced mutations and increase susceptibility to chemical-induced mtDNA mutagenesis. We conducted error-corrected, ultra-sensitive Duplex Sequencing to investigate the effects of two known nuclear genome mutagens, cadmium and Aflatoxin B1, on germline mtDNA mutagenesis in Caenorhabditis elegans. After 1,750 generations, we detected 2,270 single nucleotide mutations. Heteroplasmy is pervasive in C. elegans and mtDNA mutagenesis is dominated by C:G [->] A:T mutations generally attributed to oxidative damage, yet there was no effect of either exposure on mtDNA mutation frequency, spectrum, or trinucleotide context signature. Mitophagy may play a role in eliminating mtDNA damage or deleterious mutations, and mitophagy-deficient mutants pink-1 and dct-1 accumulated significantly higher levels of mtDNA damage compared to wild-type C. elegans after exposures. However, there were only small differences in overall mutation frequency, spectrum, or trinucleotide context signature compared to wild-type after 3,050 generations, across all treatments. These findings suggest mitochondria harbor additional previously uncharacterized mechanisms that regulate mtDNA mutational processes across generations.

genomics↗

bioRxiv2019

Bacterial Major Vault Protein homologs shed new light on origins of the enigmatic organelle

Vaults are large cone-shaped and highly conservative ribonucleoprotein complexes present in the cells of most major eukaryote clades. However, despite their wide distribution, their functions and evolutionary dynamics still remain enigmatic. Several minor functions in modulating signaling cascades and multidrug resistance phenotypes were previously discovered for eukaryotic vaults, yet nothing is known about bacterial homologs of the major vault protein (MVP), a protein that comprises the entirety of vault external surface. Using gene and protein BLAST searches in NCBI and UniProt databases we identified a number of bacterial species in prokaryotic orders Myxococcales, Cytophagales and Oscillatoriales with >50% identity to eukaryotic MVP sequences. Interestingly, all of these species are characterized by one common feature - gliding type of motility. Secondary structures of the identified proteins were predicted using RAPTORX web service and aligned via jFATCAT-flexible algorithm in the RCSB PDB Java Structure Alignment tool to elucidate structural identity. Coiled coil domain at the MVP C-terminus of all studied bacterial species resembled TolA protein of Escherichia coli by both structure and sequence. We also showed that MVP sequences from chemotrophic bacteria Myxococcales and Cytophagales contain a domain homologous to eukaryotic band-7 domain, unlike cyanobacterial and eukaryotic major vault proteins. As expected, maximum-likelihood phylogenetic trees for MVP sequences separate studied taxa into two clades - first clade contains Oscillatoriales (Cyanobacteria) and Eukaryotes and the second one contains chemotrophic bacteria. In addition, binding prediction via RAPTORX showed great multiplicity GMP and CMP nucleoside monophosphate binding pockets in Myxococcales and Cytophagales MVP, unlike eukaryotic and cyanobacterial proteins which had much lower affinity to these substrates. Due to high similarity of eukaryotic and cyanobacterial MVP sequences and a pattern of its phylogenetic distribution, we can speculate that the most likely scenario for vault appearance in eukaryotes is horizontal gene transfer from cyanobacteria. Presence of GMP and CMP binding pockets in MVP could also point to a function in depleting cytosolic nucleotide concentration which would be beneficial, for instance, during a viral infection. Further research is necessary to uncover potential functions of this enigmatic protein in bacteria and to determine its evolutionary patterns. In addition, a correlation between MVP presence and gliding motility in bacteria could also lead to elucidating selective pressures on the early evolution of this protein.

evolutionary biology↗