Evolution and metabolite signaling of fumarases (class I and II): origin, function, and subcellular targeting

This study explores the evolutionary origins of class I and II fumarases across the tree of life, focusing on the prevalence and phylogenetic patterns of their enzymes. Using a dataset of ∼21,000 complete proteomes and MMseqs2 easy-search against known fumarase sequences, we identified representative sequences for each class and constructed phylogenetic trees. Class I fumarases are found primarily in bacteria and in several eukaryotic groups, including Protozoa, SAR, and algae, with absence in fungi and archaea and low presence in plants and animals. Their patchy distribution and absence in archaea suggest horizontal gene transfer from bacteria to eukaryotes. Class II fumarases are ubiquitously distributed across bacteria, archaea, and eukaryotes. Phylogenetic and genetic analyzes suggest a closer relationship between eukaryotic class II fumarases and bacterial homologs (particularly Alphaproteobacteria) compared to archaea. These results support the hypothesis that class II fumarase originated early on in bacteria and was then inherited by vertical gene transfer by eukaryotes. Analysis of protein sequences and structures for both classes demonstrates high evolutionary conservation, consistent with their essential catalytic function. Fumarases, TCA cycle enzymes, have been implicated in DNA damage response in numerous organisms, in all domains of life. These enzymes have also been shown to be dual targeted to mitochondria and the cytosol/nucleus in eukaryotes. We have examined how these two functions are linked to the evolution of fumarases and concluded that the extramitochondrial functions and subcellular localization of fumarases were determined much later in evolution. We conclude that metabolic signaling and its specific metabolites may provide the driving force for the fumarases' dual function, dual targeting, and interaction with different entities in the cell.