Plastid-nuclear ERCnet analysis results

Plant cells rely on an interconnected network of proteins interacting at
many levels (e.g. physical enzyme complexes, gene regulatory modules, and
biosynthetic pathways). Pairs of proteins that interact at any of these
levels have been shown to exhibit phylogenetic signatures of evolutionary
rate covariation (ERC), providing a basis for detecting functional
interactions among proteins. Here, we apply ERCnet, a bioinformatic tool
for performing genome-scale ERC analyses, to predict a plant
protein-protein interactome network. We find a clustered set of proteins
that exhibit strong signatures of ERC with the plastid caseinolytic
protease (Clp) and other plastid proteostasis components, thus forming a
functional module within the network. In addition to including proteins
with known or predicted functions in protein import, transcription,
translation, and degradation in plastids, the module also includes
proteins with previously unknown molecular function, thus providing
evidence that these proteins may contribute to plastid proteostasis in
novel ways. Furthermore, perhaps the most surprising members of this
module are a set of proteins that are not thought to localize to the
plastid at all. These proteins include a mitochondrial-localized
pentatricopeptide repeat (PPR) protein with prior genetic evidence of
interaction with the mitochondrial Clp system and two nuclear-localized
actin-related proteins involved in chromatin remodeling and epigenetic
regulation of nuclear genes. We speculate that these non-plastid-localized
proteins act as mediators of organellar crosstalk and retrograde signaling
of cellular proteostasis status in plants. In summary, our results
highlight the connected nature of plant proteostasis systems and point to
a promising set of novel proteostasis protein candidates.