Translation: The universal structural core of life

Abstract

The Universal Gene Set of Life (UGSL) is common to genomes of all extant organisms. The UGSL is small, consisting of<100 genes, and is dominated by genes encoding the translation system. Here we extend the search for biological universality to three dimensions.Wecharacterize and quantitate the universality of structure ofmacromolecules that are commonto all of life.Wedetermine that around90% of prokaryotic ribosomalRNA(rRNA)formsa commoncore,whichis thestructuraland functional foundation of rRNAs of all cytoplasmic ribosomes.We have established a database, whichwe call the Sparse and Efficient Representation of the Extant Biology (the SEREB database). This database contains complete and cross-validated rRNAsequences of species chosen, as far as possible, to sparsely and efficiently sample all known phyla. Atomic-resolution structures of ribosomes provide data for structural comparison and validation of sequence-based models.We developed a similarity statistic called pairing adjusted sequence entropy, which characterizes paired nucleotides by their adherence to covariation and unpaired nucleotides by conventional conservation of identity. For canonically paired nucleotides the unit of structure is the nucleotide pair. For unpaired nucleotides, the unit of structure is the nucleotide. By quantitatively defining the common core of rRNA, we systematize the conservation and divergence of the translational system across the tree of life, and can begin to understand the unique evolutionary pressures that cause its universality. We explore the relationship between ribosomal size and diversity, geological time, and organismal complexity.