AbstractThe control of protein homeostasis (a.k.a. proteostasis) is associated with the primary functions of life, and therefore with evolution. However, it is unclear how the cellular proteostasis has evolved to adjust the protein biogenesis needs with environmental constraints. Herein, we describe an approach to evaluate proteostasis during evolution, and show that the proteostasis network (PN) represents a reliable metric to i) deconvolute the life forms into Archaea, Bacteria and Eukaryotes and ii) assess the evolution rates among species, without the need for rRNA sequences. This method for phylogenetic comparison relies on the use of semantic graphs to evaluate PN complexity. This stands as a novel strategy for taxonomic classification, based on the analysis of 94 Eukaryotes, 250 Bacteria and 93 Archaea genome sequences. A functional analysis was used as a powerful phylogenetic tool that echoes with species complexity. It provides information about species divergence and indicates the taxonomic clades that evolved faster than others did. Phyla-specific PN were identified, suggesting that PN complexity correlates with the grade of evolution the species have reached. Individual components, however, such as the heat shock proteins (HSP) do not accurately mark evolution. We analyzed gene conservation, gain or loss that occurred throughout PN evolution, which reveals a dichotomy within the PN conserved parts (e.g. chaperones), but also with species-specific modules. Since the PN is implicated in cell fitness, aging control and the onset of several diseases, it could be used as a metric to tackle gain-of-functions mechanisms and their biological impact.
Species‐specific clonality in east Asian island flora: Phylogenetic and environmental constraints
