Deep shifts in Evolutionary Rate Trajectories of Ancient Bacterial Genes

Reconstructing ancestral gene repertoires from current bacterial genomes only reveals the genes that have survived. Those lost from the record are unknown. Genetic pressures alter not just between lineages, but also over time. To examine evolutionary rate trajectories across 528 genes in the Last Bacterial Common Ancestor (LBCA), researchers divided these genes into five calibrated taxonomic intervals: phylum, class, order, family, and genus. These intervals span about 2.1 billion years of bacterial evolution.

Distinct rate trajectories emerge across bacterial history, organized into four clusters. The Decelerating and Class-Peaking clusters are mostly made up of genes involved in Genetic Information Processing. Conversely, the Constant and Accelerating clusters are richer in genes related to Metabolism. Specifically, the Decelerating cluster includes core informational machinery, like translation initiation factors and components of the expressome, the molecular complex binding transcription and translation. This suggests that transcription-translation interfaces stabilized early in bacterial life.

Cofactor dependence and biosynthesis are separated in the clusters. Biosynthetic pathways creating metal cofactors, such as heme, molybdopterin, and cobalamin, are found in the Constant and Accelerating clusters, but more proteins rely on inorganic cofactors in the Decelerating and Class-Peaking clusters. This separation aligns with the change in metal availability following the Great Oxidation Event, unveiling genomic signatures of bacterial metabolism evolving in harmony with planetary geochemistry.