In every plant cell, an orchestra plays where the musicians are the same but the scores differ from species to species. The main instrument of this orchestra is the 26S proteasome, a large protein machine that destroys tagged proteins. It exists in all eukaryotes, and its structure is remarkably conserved: from yeast to humans, the details have barely changed. But in plants, the number of genes encoding proteasome subunits varies widely, and until now it was unclear how these duplications affect regulation.
The authors assembled the genomes of 18 species of Viridiplantae, from the unicellular alga Chlamydomonas reinhardtii to flowering plants, and using homology searches identified all genes for 26S proteasome subunits. For each subunit family, they built alignments and phylogenetic trees, then reconciled them with the species tree to reconstruct the history of duplications. They scanned the promoters of proteasome genes for enrichment of short DNA motifs, comparing their frequency near the transcription start site with the genomic background. Additionally, they used data on post-translational modifications, predictions of intrinsically disordered regions, and calculations of electrostatic potential.
In 16 of the 18 species, duplicated proteasome genes were found, and the duplication patterns were species-specific and mostly recent. Ancient whole-genome duplications had almost no effect on the expansion of the family, but recent ones, for example in mosses or legumes, left a mark. At the protein level, selection was purifying: only four cases out of 886 showed signs of positive selection. Differences between paralogs boiled down to fine-tuning of the surface electrostatic potential and changes in phosphorylation sites. Regulation diverged much more: paralogs responded differently to stress, and this trend can be traced from mosses to flowering plants.
The trb4 trb5 mutants were hypersensitive to a proteasome inhibitor, and their induction of proteasome genes was impaired. Finally, coevolution analysis revealed a network of 386 proteins evolving in concert with the proteasome and enriched in the same regulatory motifs. This means that the proteasome is embedded in a broader network that adapts to the needs of each species.
The work shows for the first time that in plants, the conserved protein degradation machine evolves not by changing the proteins themselves but through rewiring of regulatory logic. It's as if the musicians in the orchestra remained the same but the conductor changed the scores: in one species, the proteasome is more active in response to drought, in another to cold. The discovery of the role of TRB proteins in proteasome regulation adds a new layer to our understanding of how the cell coordinates proteostasis with other processes, including the cell cycle and photosynthesis. For now, this is fundamental knowledge, but it sets the direction for breeding stress-resistant plants, because proteostasis is critical for survival under adverse conditions.
In Arabidopsis, the promoters of proteasome genes contain a motif that also shows up in telomeres, the end sections of chromosomes. Proteins that normally guard the ends of chromosomes turned out to be capable of switching on proteasome genes.
Not published on arXiv. Here are its page, the PDF and the formalization: you can check it yourself, not only read our account.