Biology subjects

Cisneros, A. F.

Publications and source records attributed to Cisneros, A. F..

3 recordsLinked to original sources

bioRxiv2025

The effect of allelic molecular interactions on phenotypic dominance

Mendelian genetics provides us with a framework for studying allelic dominance relationships at a locus at the phenotypic level. These dominance relationships result from different molecular factors, including the mapping of molecular activity onto fitness. For homomeric proteins, physical interactions between alleles provide a mechanism by which one allele can have a dominant effect on the activity of the other. Here, we refer to the effect of these interactions as molecular dominance and examine how they determine total protein activity and contribute to phenotypic dominance. The relative impact of such molecular dominance effects depends on the proportion of subunits that heteromerize relative to those that form homomers. In turn, we show how the effect of physical interactions on phenotypic dominance depends on the function linking protein activity to fitness. Our results show the complex relationships between molecular and phenotypic dominance and highlight the fundamental difference in dominance landscapes for monomeric and homomeric proteins.

genetics↗

bioRxiv2025

Co-translational assembly promotes functional diversification of paralogous proteins

Homomeric proteins are ubiquitous and mediate myriads of cellular functions. When a gene encoding a homomer duplicates, the resulting paralogs can either form distinct homomers, or evolve into a heteromer containing both paralogs. While such events have extensively shaped proteomes, the molecular mechanisms driving these fates and their associated functional consequences remain largely unknown. Here, we conducted a comprehensive phylogenomic analysis tracing gene duplication histories of 7,377 human paralogs across the eukaryotic lineage and identified their fates using protein interaction data. Simulations and data analyses show that cellular constraints must act as barriers to disfavor heteromerization and promote homomerization. We found that multiple cellular and molecular constraints can serve as barriers, including the lack of co-expression and co-localization. The main barrier, however, is co-translational assembly, which naturally promotes the self-assembly of each paralog from its corresponding mRNA, thus hindering heteromerization. We further established that heteromerization constrains functional divergence, with homomeric paralogs exhibiting stronger signatures of adaptive evolution and functional divergence compared to heteromeric paralogs. Together, these findings identify key biochemical and cellular properties that explain protein function diversification following gene duplication. One Sentence SummaryCo-translational assembly drives the selective homo-oligomerization of paralogs, which in turn promotes their functional divergence. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=180 HEIGHT=200 SRC="FIGDIR/small/634331v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@b17418org.highwire.dtl.DTLVardef@3d0a61org.highwire.dtl.DTLVardef@1747aeaorg.highwire.dtl.DTLVardef@31b931_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2023

Mutational biases contribute to the neutral complexification of protein interaction networks following gene duplication

Biological systems can gain complexity over time. While some of these transitions are likely driven by natural selection, the extent to which they occur without providing an adaptive benefit is unknown. At the molecular level, one example is heteromeric complexes replacing homomeric ones following gene duplication. Here, we build a biophysical model and simulate the evolution of homodimers and heterodimers following gene duplication using distributions of mutational effects inferred from available protein structures. We keep the specific activity of each dimer identical, so their concentrations drift neutrally without new functions. We show that for more than 60% of tested dimer structures, the relative concentration of the heteromer increases over time due to mutational biases that favor the heterodimer. However, allowing mutational effects on synthesis rates and differences in the specific activity of homo- and heterodimers can limit or reverse the observed bias toward heterodimers. Our results show that the accumulation of more complex protein quaternary structures is likely under neutral evolution, and that natural selection would be needed to reverse this tendency.

systems biology↗