Expression attenuation as a mechanism of robustness against gene duplication

Abstract

Gene duplication is ubiquitous and a major driver of phenotypic diversity across the tree of life, but its immediate consequences are not fully understood. Deleterious effects would decrease the probability of retention of duplicates and prevent their contribution to long-term evolution. One possible detrimental effect of duplication is the perturbation of the stoichiometry of protein complexes. Here, we measured the fitness effects of the duplication of 899 essential genes in the budding yeast using high-resolution competition assays. At least 10% of genes caused a fitness disadvantage when duplicated. Intriguingly, the duplication of most protein complex subunits had small to nondetectable effects on fitness, with few exceptions. We selected four complexes with subunits that had an impact on fitness when duplicated and measured the impact of individual gene duplications on their protein–protein interactions. We found that very few duplications affect both fitness and interactions. Furthermore, large complexes such as the 26S proteasome are protected from gene duplication by attenuation of protein abundance. Regulatory mechanisms that maintain the stoichiometric balance of protein complexes may protect from the immediate effects of gene duplication. Our results show that a better understanding of protein regulation and assembly in complexes is required for the refinement of current models of gene duplication.

Multilayered regulation of proteome stoichiometry

“…2) and that the stability of the subunit corresponds to the state of assembly: (stable) fully assembled complex ≥ subcomplex > unassembled monomeric subunit (unstable). It is further supported by the observation of a similar degree of dosage compensation between subunits of the same subcomplex of the 26S proteasome (Ascencio et al 2021). Notably, the second layer does not apply to dosage-sensitive complexes including tubulin, whose excess is associated with toxicity, and thus its stoichiometry is tightly controlled in the first layer (Katz et al 1990;Li et al 2014;Makanae et al 2013).…”

“…Indeed, overexpression experiments have confirmed this hypothesis in 13 out of 49 tested subunit pairs (27%) (Makanae et al 2013). It is unclear whether the other 36 complexes are compensated, thereby avoiding growth defects, but recent results suggest that dosage compensation contributes to cellular robustness (Ascencio et al 2021). The effect of gene duplication on fitness was measured for 899 Fig.…”

“…B Genetic perturbations caused by increased gene dosage due to ane-uploidy and multicopy plasmids. They affect cellular systems differently (Bonney et al 2015), and not all of the compensated proteins identified in these conditions overlap (Ishikawa et al 2017) essential genes in budding yeast, and it was found that only about 10% of the genes were associated with fitness disadvantage and that the effect on fitness was limited because genes encoding subunits were protected by dosage compensation (Ascencio et al 2021). Therefore, it is concluded that the primary function of protein-level dosage compensation is to fine-tune stoichiometry of multiprotein complex subunits.…”

Natural variation in the consequences of gene overexpression and its implications for evolutionary trajectories

“…One model to explain this enrichment is that perturbing stoichiometric balances will perturb complex assembly and function ( Papp et al, 2003 ; Veitia et al, 2008 ; Birchler and Veitia, 2012 ; Moriya, 2015 ). Cells have mechanisms to control the dosage of some of these proteins, yet high-copy OE can still overwhelm these mechanisms in the cell ( Li et al, 1995 ; Li et al, 1996 ; Fewell and Woolford, 1999 ; Hose et al, 2015 ; Ascencio et al, 2021 ). Protein OE can also force promiscuous interactions, perturbing protein interaction networks.…”

Barcode Fusion Genetics-Protein-fragment Complementation Assay (BFG-PCA): tools and resources that expand the potential for binary protein interaction discovery

“…However, we should take into account the targeted space (the proteasome and nuclear pore complexes) in this study. It is known for instance that the subunits in the proteasome are regulated at the post transcriptional level (Ascencio et al 2021) , which means that higher transcription levels from the ADH1 promoter may not influence PPIs. Also, subunits of these two protein complexes may be more expressed already than many other proteins, leaving little room for signal improvement with this promoter.…”