Ribosomal protein sequence analysis reveals the order of evolution of bacterial classes, direct lineage of Cyanobacteria and Chloroplasts and that LUCA was an Actinobacteria

Abstract

Search vectors composed primary of Gly, Ala, Arg, and Pro residues (GARP) distributed across the entire protein sequence retrieve 98% of each of the ribosomal proteins in bacterial species with no false “hits”. Different combinations of G, A, R and P and insertions or deletions differentiate each ribosomal protein from all others. We are able to identify site mutations that subdivide each ribosomal protein ensemble into the individual classes of bacteria. For example, four fold variation in a single sequence position in S4 separates 490 gram‐positive bacteria that have Y and F in this position and 717 gram‐negative bacteria that have W in this position from 68 cyanobacteria and 601 chloroplasts that have an H in this position. Detection of co‐evolution of amino acids in four sequence positions makes it possible to divide the 1876 ribosomal proteins into 25 classes. Further subdivision into orders, families, genus, and species is trivial. While there are significant differences between the sequences of the ribosomal proteins in different classes of bacteria, within each class the amino acid sequences have remained highly conserved for millions of years. We have found that the total GARP content of the ribosomal proteins of each class is a marker of the order of evolution and that the last universal common ancestor (LUCA) appears to have been an Actinobacteria.