| Popis: |
Almost all eukaryotes contain mitochondria, and many contain plastids, playing vital roles in the bioenergetic and metabolic processes that power complex life. Since their endosymbiotic origins, the genomes of both organelles have been reduced, with genes being lost or transferred to the host cell nucleus from organelle DNA (oDNA) to different extents in different species. Why some genes are retained in oDNA and some lost remains a debated question. Long-standing hypotheses include the preferential retention of genes encoding hydrophobic products and those most central to redox regulation , but quantitative testing of these and other ideas remains absent. Here we harness over 15k oDNA sequences and over 300 whole genome sequences with tools from structural biology, bioinformatics, machine learning, and Bayesian model selection to reveal the properties of protein-coding genes that shape oDNA evolution. We find striking symmetry in the features predicting mitochondrial (mtDNA) and plastid (ptDNA) gene retention. Striking symmetry exists between the two organelle types: gene retention patterns in both are predicted by the hydrophobicity of a protein product and its energetic centrality within its protein complex, with additional influences of nucleic acid and amino acid biochemistry. Supporting this generality, models trained with one organelle type successfully predict gene retention in the other, and these features also distinguish gene profiles in independent endosymbiotic relationships. The identification of these features both provide quantitative support for several existing evolutionary hypotheses, and suggest new biochemical and biophysical mechanisms influencing organelle genome evolution. |
