Evolution of the ribosomal common core
Bernier, Chad R.
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Understanding the origin of life requires understanding the origin of translation, which in turn, requires understanding the origin of the ribosome. Ribosomes are complex structures consisting of hundreds of thousands of atoms. Here, we describe how we organized ribosomal structures and information into a broad database, RiboZones. We also describe a new visualization web app, RiboVision. RiboZones and RiboVision are productivity tools that lower the learning curve for ribosomal research. RiboZones makes the ribosome more accessible. RiboVision especially helps create beautiful publication ready figures in a fraction of the labor and time previously required. It is only through the creation of RiboZones and RiboVision through which the rest of this dissertation became feasible. We constructed a high-quality sequence alignment of ribosomal sequences for both the LSU and the SSU rRNA. Each ribosomal sequence is complete, allowing detailed, low background statistics to be computed. The sequence alignment broadly samples the tree of life according to available data. The alignment was adjusted for maximum agreement with 3D superimpositions of multiple ribosomal structures. We defined a nucleotide-level definition of the common core of the ribosome, as the RNA that is present in 95% of the sequences in our alignment. Multiple versions of the common core were created, including the universal common core, the prokaryotic common core, and domain specific common cores. The definition allows statistics to be computed for various use-cases. For example, with RiboVision visualization technology, it is possible to see which helices are optional, in which of the three domains of life, and what the minimum helical length is for each helix. We discovered that ribosomal RNA grows mostly by helix extension and helix insertion. When a helix is inserted, it minimally perturbs the underlying helix. We call this pattern ‘insertion fingerprints’. Insertion fingerprints are found throughout the common core and the eukaryotic expansion segments. Insertion fingerprints were used to divide the ribosomal RNA into units called ancestral expansion segments (AES’s). AES’s make ideal structural, functional, and evolutionary units. The AES’s are arranged into the first complete experimentally testable model of ribosomal evolution. The model can be refined over time as new information is discovered.