Abstract
Universally conserved positions in ribosomal proteins have significant biases in amino acid usage, likely indicating the expansion of the genetic code at the time leading up to the most recent common ancestor(s) (MRCA). Here, we apply this principle to the evolutionary history of the ribosome before the MRCA. It has been proposed that the experimentally determined order of assembly for ribosomal subunits recapitulates their evolutionary chronology. Given this model, we produce a probabilistic evolutionary ordering of the universally conserved small subunit (SSU) and large subunit (LSU) ribosomal proteins. Optimizing the relative ordering of SSU and LSU evolutionary chronologies with respect to minimizing differences in amino acid usage bias, we find strong compositional evidence for a more ancient origin for early LSU proteins. Furthermore, we find that this ordering produces several trends in specific amino acid usages compatible with models of genetic code evolution.
Highlights
The ribosome is a large complex of RNA and several proteins, composed of two major subunits, the large (LSU) and small (SSU) subunits
Both subunits are highly conserved in all domains of life, and contain several proteins found in every living organism [1], suggesting the core ribonucleoprotein structure evolved before the time of the most recent common ancestor(s) (MRCA)
While previous studies have analyzed the overall bias at these positions [5], recapitulating the evolutionary chronology of universal ribosomal proteins from their observed subunit assembly maps [6] allows for a deeper, longitudinal view of changes in amino acid usage
Summary
The ribosome is a large complex of RNA and several proteins, composed of two major subunits, the large (LSU) and small (SSU) subunits. As both the LSU and SSU have independent subunit assembly maps, there exists no a priori way to determine the relative ordering of proteins between each chronology; assuming that each subunit would be subject to the same pressures of an evolving genetic code, these can be aligned via minimization of the pairwise difference in overall amino acid usage bias observed at each respective chronology position.
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