Biology subjects

Voronka, A.

Publications and source records attributed to Voronka, A..

3 recordsLinked to original sources

bioRxiv2026

From life history to proteome via mutagenesis: an ecological footprint in genome evolution

Species differ in longevity, physiology, and social organization, and these properties expose them to distinct endogenous and environmental mutagens. Mutational spectra generated by these processes can shape downstream molecular evolution, influencing synonymous nucleotide composition, codon usage, and even amino acid composition. Tracing this signal from life history to proteome through mutagenesis could reveal how mutational pressure interacts with the fitness landscape, including the direction of molecular change and the extent to which proteins remain functional while following mutational biases. Here, building on the recently identified age-associated mitochondrial A>G mutational signature in mammals, we test the universality of this signature and its downstream effects on genome and proteome evolution by comparing long-lived termites with short-lived non-termite cockroaches. We find that termite mtDNA exhibits a stronger A>G mutational signature than that of non-termite cockroaches, accompanied by coordinated shifts in synonymous nucleotide composition, codon usage, and amino acid composition. Our results show that ecological and life-history-associated mutational pressures can be transmitted through a hierarchy from mutational spectra to nucleotide composition and ultimately to proteome evolution. Mitochondrial genomes may therefore function not only as records of ancestry but also as molecular archives of the biological conditions under which species evolve.

evolutionary biology↗

bioRxiv2026

Mutational bias shapes protein evolution across RNA viruses

Mutational biases can influence genome composition, but their contribution to protein evolution remains difficult to quantify. Here we utilize a nearly neutral framework that translates nucleotide mutational spectra into expected amino acid substitution patterns and equilibrium amino acid compositions. Using SARS-CoV-2 as a model system, we show that the viral mutational spectrum explains more than 50% of the variation in observed single-nucleotide amino acid substitutions and predicts the overall direction of proteome-wide amino acid composition change during the COVID-19 pandemic. The predictive power of the model varies with selection regime: effectively neutral and weakly deleterious substitutions conform most closely to the mutational expectation, whereas strongly constrained sites and mutational hotspots show larger deviations. This indicates that departures from the nearly neutral baseline provide a quantitative proxy for purifying and positive selection. Extending the analysis across 34 RNA virus species, we find that positive-sense, negative-sense and double-stranded RNA viruses differ systematically in their mutational spectra, and that these differences are associated with predictable shifts in proteome composition. The same relationship is detectable in RNA-dependent RNA polymerase sequences from more than 77,000 viral species. These results indicate that taxon-specific mutational bias contributes persistently to protein evolution across evolutionary scales.

bioinformatics↗

bioRxiv2022

The butterfly effect: mutational bias of SARS-CoV-2 affects its pattern of molecular evolution on synonymous and nonsynonymous levels

Evolution is a function of mutagenesis and selection. To analyse the role of mutagenesis on the structure of the SARS-CoV-2 genome, we reconstructed the mutational spectrum, which was highly C>U and G>U biased. This bias forces the SARS-CoV-2 genome to become increasingly U-rich unless selection cancels it. We analysed the consequences of this bias on the composition of the most neutral (four-fold degenerate synonymous substitutions) and the least neutral positions (nonsynonymous substitutions). The neutral nucleotide composition is already highly saturated by U and, according to our model, it is at equilibrium, suggesting that in the future, we dont expect any more increase in U. However, nonsynonymous changes continue slowly evolve towards equilibrium substituting CG-rich amino-acids ("losers") with U-rich ones ("gainers"). This process is universal for all genes of SARS-CoV-2 as well as for other coronaviridae species. In line with the direction mutation pressure hypothesis, we show that viral-specific amino acid content is associated with the viral-specific mutational spectrum due to the accumulation of effectively neutral slightly deleterious variants (losers to gainers) during the molecular evolution. The tuning of a protein space by the mutational process is expected to be typical for species with relaxed purifying selection, suggesting that the purging of slightly-deleterious variants in the SARS-CoV-2 population is not very effective, probably due to the fast expansion of the viral population during the pandemic. Understanding the mutational process can help to design more robust vaccines, based on gainer-rich motifs, close to the mutation-selection equilibrium.

evolutionary biology↗