Probing co-evolution of ribosomal proteins through structural phylogeny

Ribosomes are
highly conserved macromolecular machines at the domain level. This necessitates
that ribosomal proteins also exhibit conservation in structure and function
across genus and species. Specifically, ribosomal proteins are in contact with
each other and ribosomal RNA (rRNA) in either the small or large ribosomal
subunit. These contact points thus provide constraints in evolution and natural
selection, and may have resulted in co-evolution. Given that coevolution
between different ribosomal proteins could manifest as similarity in protein
structure, the structures of the different ribosomal proteins could be obtained
through a homology search server, Phyre2 to provide the foundational
data for a cross-comparison of ribosomal protein structure for understanding
the selection pressure exerted on the ribosomal proteins. Specifically, multiple
ribosomal proteins and rRNA interact with each other within the ribosome and
the contact sites at which ribosomal protein and rRNA interact could serve as
points at which selection pressure could tune the evolutionary trajectories of
the ribosomal protein and rRNA. Thus, co-evolution between ribosomal proteins
and between ribosomal proteins and rRNA would manifest as structural motifs
tuned for binding with each other or where protein-protein and protein-rRNA
interactions result in conserved structural motifs for interaction.