Ribosomal History Reveals Origins of Modern Protein Synthesis (original) (raw)
Figure 1
Experimental strategy.
The flow diagram in the left describes the phylogenetic reconstruction of trees of rRNA molecules and substructures. The structures of rRNA molecules were first decomposed into substructures, including helical stem tracts and unpaired regions. Structural features of these substructures (e.g., length) were coded as phylogenetic characters and assigned character states according to an evolutionary model that polarizes character transformation towards an increase in molecular order (character argumentation). Coded characters (s) are arranged in data matrices, which can be transposed for cladistic analyses. Phylogenetic analysis using MP methods generate rooted phylogenetic trees of either molecules or substructures. Only trees of substructures are presented in this study. The flow diagram in the right shows the reconstruction of trees of proteomes and trees of protein domain structures. A census of domain structures in proteomes of hundreds of completely sequenced organisms is used to compose a data matrix and its transposed matrix, which are then used to build phylogenomic trees describing the evolution of individual protein structures and entire molecular repertoires, respectively. Elements of the matrix (g) represent genomic abundances of architectures (at FSF level of hierarchical classification of structure) in proteomes. Trees of proteomes will be described elsewhere, but are largely congruent with traditional classification. Embedded in the tree of rRNA substructures and tree of protein domains are timelines that assign age to molecular structures. These ages can be “painted” onto 2D or 3D structural models of the ribosome, generating evolutionary heat maps. Evolutionary information from RNA and protein structures is finally combined to generate a model of structural evolution.