Extreme variation in rates of evolution in the plastid Clp protease complex

Abstract

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. The clpP1 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 clpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find that clpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g. a loss of introns and RNA-editing sites) within seed plants. Although clpP1 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 Silene, which has highly elevated and heterogeneous rates of clpP1 evolution. We confirmed that clpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergent Silene species. Additionally, there is a tight correlation between amino acid substitution rates in clpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting continuing selection on interactions within this complex.

Cytonuclear Genetic Incompatibilities in Plant Speciation

“…ACCase is involved in fatty acid biosynthesis. Both complexes are composed of one plastid-encoded SU and several nuclear-encoded SUs [14,31]. Generally, the gene sequences of accD and clpP1 (plastid genes) are relatively conserved among angiosperms but, in some independent lineages, evolution rates were found to be accelerated (quoted by [14]).…”

“…Thus, coevolution between nuclear-encoded and plastid-encoded SUs of Clp and ACCase complexes is suggested by signature of positive selection for compensatory mutations in Silene nuclear genes of these complexes [14]. Williams et al (2019) conducted a study on the Clp complex across a broad range of angiosperms and observed correlated rates of accelerated evolution in the plastid-encoded and nuclear-encoded SUs [31]. Given these results, nuclear genes encoding SUs of plastid complex seem to experience positive selection to maintain coadaptation with their fast-evolving plastid genes.…”

“…This highlights the diversity of cytonuclear coevolution patterns [15,32]. Coevolution signals in plants were mostly found in protein complexes involving plastid genes with accelerated evolution, such as genes encoding essential plastidic factors (ycf1 and ycf2 [29]), RNA polymerase SU, ribosomal proteins [18], accD [14] and clpP1 [28,31]. Concerning the genes encoding components of the photosynthetic apparatus, this coevolution pattern was less evident, due to their high sequence conservation and low rate of sequence evolution [11,12,14,28].…”

“…The extreme degree of conservation of the genes encoding photosynthetic apparatus suggests that they evolve under genetic drift and/or strong purifying selection [11,12]. Yet, positive selection was identified for some specific genes and in particular lineages, pointing out a potential role of these genes on local adaptation [11,12,31]. For example, positive selection was found in the photosynthetic rbcL plastid gene, encoding a SU of the essential Rubisco enzyme [12,77].…”

“…Distinguishing between positive selection and relaxed purifying selection is difficult, as they lead to the same pattern of increase of d N /d S ratio [31]. Looking at the variation of intra-and interspecific sequences can be a promising approach, since in the case of positive selection, the fixation of NS substitutions leads to an increase in ω between species (i.e., interspecific divergence), compared to intraspecific polymorphism [18].…”