Computing the origin and evolution of the ribosome from its structure – uncovering processes of macromolecular accretion benefiting synthetic biology

Publication date: Available online 26 July 2015 Source:Computational and Structural Biotechnology Journal Author(s): Gustavo Caetano-Anollés, Derek Caetano-Anollés Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features show patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive pro...
Source: Computational and Structural Biotechnology Journal - Category: Biotechnology Source Type: research