Looking back to look forward: protein–protein interactions and the evolution of development

Abstract

The evolutionary modification of development was fundamental in generating extant plant diversity. Similarly, the modification of development is a path forward to engineering the plants of the future, provided we know enough about what to modify. Understanding how extant diversity was generated will reveal productive pathways forward for modifying development.Here, I discuss four examples of developmental pathways that have been remodeled by changes to protein-protein interactions. These are cases where changes to developmental pathways have been paralleled by recent changes, selected for or engineered by humans. Extant plant diversity represents a vast treasure trove of molecular solutions to ecological problems. Mining this treasure trove will allow for the intentional modification of plant development for solving future problems.

Repressor for hire! The vital roles of TOPLESS‐mediated transcriptional repression in plants

“…Interactions between TPL and proteins with RDs have been identified in taxa from algae through to angiosperms, suggesting that this repression mechanism has been evolutionarily conserved since before the earliest land plants (> 450 million yr) (Martin-Arevalillo et al, 2017). Changes to protein-protein interactions have been the catalyst for developmental innovation throughout evolution (Bartlett, 2020). TPL interactors are enriched for RDs (Causier et al, 2012b) and the acquisition of an RD, a comparatively small motif, may have enabled TFs to recruit the pre-existing TPL corepressor into new pathways as they arose during evolution, driving innovation.…”

Functional Diversification of Populus FLOWERING LOCUS D-LIKE3 Transcription Factor and Two Paralogs in Shoot Ontogeny, Flowering, and Vegetative Phenology

“…In Populus, FT2 is expressed in leaves and rapidly downregulated by short days (SDs), whereas FT1 expression peaks during winter in multiple tissues within winter buds (Böhlenius et al, 2006;Hsu et al, 2011). Changes in cis-regulatory sequences have generally been considered the predominant mechanism for developmental evolution, but increasing evidence supports a role for protein coding changes and both types of sequence changes can be necessary for the evolution of new transcriptional circuits (Lynch and Wagner, 2008;Bartlett, 2020;Britton et al, 2020). Although their divergent seasonal expression patterns could be sufficient for functional diversification of the Populus FT paralogs, their encoded proteins are not fully equivalent.…”

Predicted landscape of RETINOBLASTOMA‐RELATED LxCxE‐mediated interactions across the Chloroplastida

“…An important mechanism by which the functions of TRs evolve is by changes in auxiliary protein domains (Romani & Moreno, 2020), such as RbN and RbC, which may impact interactions with other proteins, oligomerization, protein stability, etc. (Bartlett, 2019). Pocket proteins such as pRB and RBR lack DNA‐binding domains and as such are not considered ‘classic’ TFs; however, they are bona fide TRs for their capacity to act synergistically or antagonistically with TFs to regulate gene expression output (Cruz‐Ramírez et al., 2012; Goupille et al., 2017; Gutzat et al., 2011; Johnston et al., 2008; Lang et al., 2021; Matos et al., 2014; Sanidas et al., 2022; Zamora‐Zaragoza, Klap, Heidstra, et al., 2021), thus we speculate that if the pocket and RbN regions of RBR proteins interact and function in a similar way as metazoan pRB, therefore, the loss and/or modification of these regions in the aforementioned streptophyte algae RBR orthologs could impinge on RBR structural regulation and possibly function; however, more research is needed to characterize the RbN region in RBR proteins to determine how these modifications could influence RBR function.…”