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1. Uvr motifs regulate the chloroplast Clp chaperone–protease system

   https://doi.org/10.1016/j.tplants.2024.09.015  

   Annis, Marissa Y; Ravenburg, Claire M; van_Wijk, Klaas J (March 2025, Trends in Plant Science)
2. Extreme variation in rates of evolution in the plastid Clp protease complex

   https://doi.org/10.1111/tpj.14208  

   Williams, Alissa M.; Friso, Giulia; van Wijk, Klaas J.; Sloan, Daniel B. (January 2019, The Plant Journal)

   Summary 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 (clpP1) and multiple nuclear genes. TheclpP1gene 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 ofclpP1molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find thatclpP1has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns andRNA‐editing sites) within seed plants. AlthoughclpP1is 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 genusSilene, which has highly elevated and heterogeneous rates ofclpP1evolution. We confirmed thatclpP1is expressed as a stable protein and forms oligomeric complexes with the nuclear‐encoded Clp subunits, even in one of the most divergentSilenespecies. Additionally, there is a tight correlation between amino acid substitution rates inclpP1and the nuclear‐encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex. 

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3. Rapid sequence evolution is associated with genetic incompatibilities in the plastid Clp complex

   https://doi.org/10.1007/s11103-022-01241-4  

   Abdel-Ghany, Salah E.; LaManna, Lisa M.; Harroun, Haleakala T.; Maliga, Pal; Sloan, Daniel B. (February 2022, Plant Molecular Biology)
4. Role of Diffusion in Unfolding and Translocation of Multidomain Titin I27 Substrates by a Clp ATPase Nanomachine

   https://doi.org/10.1021/acs.jpcb.8b10282  

   Javidialesaadi, Abdolreza; Flournoy, Shanice M.; Stan, George (March 2019, The Journal of Physical Chemistry B)
5. Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms

   https://doi.org/10.1016/j.ympev.2022.107395  

   Williams, Alissa M.; Carter, Olivia G.; Forsythe, Evan S.; Mendoza, Hannah K.; Sloan, Daniel B. (March 2022, Molecular Phylogenetics and Evolution)