Description:
<jats:title>Summary</jats:title><jats:p><jats:bold>Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multi‐subunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid‐encoded gene (</jats:bold><jats:italic><jats:bold>clpP1</jats:bold></jats:italic><jats:bold>) and multiple nuclear genes. The</jats:bold><jats:italic><jats:bold>clpP1</jats:bold></jats:italic> <jats:bold>gene is highly conserved across most green plants, but it is by far the fastest evolving plastid‐encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history of</jats:bold><jats:italic><jats:bold>clpP1</jats:bold></jats:italic> <jats:bold>molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find that</jats:bold><jats:italic><jats:bold>clpP1</jats:bold></jats:italic> <jats:bold>has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns and</jats:bold><jats:styled-content style="fixed-case"><jats:bold>RNA</jats:bold></jats:styled-content><jats:bold>‐editing sites) within seed plants. Although</jats:bold><jats:italic><jats:bold>clpP1</jats:bold></jats:italic> <jats:bold>is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genus</jats:bold><jats:italic><jats:bold>Silene</jats:bold></jats:italic><jats:bold>, which has highly elevated and heterogeneous rates of</jats:bold><jats:italic><jats:bold>clpP1</jats:bold></jats:italic> <jats:bold>evolution. We confirmed that</jats:bold><jats:italic><jats:bold>clpP1</jats:bold></jats:italic> <jats:bold>is expressed as a stable protein and forms oligomeric complexes with the nuclear‐encoded Clp subunits, even in one of the most divergent</jats:bold><jats:italic><jats:bold>Silene</jats:bold></jats:italic> <jats:bold>species. Additionally, there is a tight correlation between amino acid substitution rates in</jats:bold><jats:italic><jats:bold>clpP1</jats:bold></jats:italic> <jats:bold>and the nuclear‐encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.</jats:bold></jats:p>