Divergent evolution of the M3A family of metallopeptidases in plants

Abstract

Plants, as stationary organisms, have developed mechanisms allowing them efficient resource reallocation and a response to changing environmental conditions. One of these mechanisms is proteome remodeling via a broad peptidase network present in various cellular compartments including mitochondria and chloroplasts. The genome of the model plant Arabidopsis thaliana encodes as many as 616 putative peptidase-coding genes organized in 55 peptidase families. In this study, we describe the M3A family of peptidases, which comprises four members: mitochondrial and chloroplastic oligopeptidase (OOP), cytosolic oligopeptidase (CyOP), mitochondrial octapeptidyl aminopeptidase 1 (Oct1) and plant-specific protein of M3 family (PSPM3) of unknown function. We have analyzed the evolutionary conservation of M3A peptidases across plant species and the functional specialization of the three distinct subfamilies. We found that the subfamily-containing OOP and CyOP-like peptidases, responsible for oligopeptide degradation in the endosymbiotic organelles (OOP) or in the cytosol (CyOP), are highly conserved in all kingdoms of life. The Oct1-like peptidase subfamily involved in pre-protein maturation in mitochondria is conserved in all eukaryotes, whereas the PSPM3-like protein subfamily is strictly conserved in higher plants only and is of unknown function. Specific characteristics within PSPM3 sequences, i.e. occurrence of a N-terminal transmembrane domain and amino acid changes in distal substrate-binding motif, distinguish PSPM3 proteins from other members of M3A family. We performed peptidase activity measurements to analyze the role of substrate-binding residues in the different Arabidopsis M3A paralogs.

Profiling thimet oligopeptidase‐mediated proteolysis in Arabidopsis thaliana

“…The double mutant was used in comparison with WT instead of top single mutants due to their documented shared roles in ETI and PCD (Kmiec et al, 2013; Moreau et al, 2013; Polge et al, 2009; Westlake et al, 2015). While TOP1 and TOP2 have different subcellular localizations, their functional overlap and high sequence similarity (92%) suggest a potential for redundant substrates (Kmiec et al, 2016; Moreau et al, 2013). The use of the double mutant also ensures the detection of TOP substrate accumulation compared to the WT.…”

“…Thimet oligopeptidases (TOPs) are zinc-dependent peptide hydrolases with a conserved HEXXH active site motif (Gomiz-R€ uth, 2009;Kmiec et al, 2016). These metallopeptidases are critical components in plant response to oxidative stress triggered by pathogens or abiotic factors and are required for a fully functioning immune response to certain pathogens (Moreau et al, 2013;Westlake et al, 2015).…”

Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium ‘fitti’) among closely related coral hosts

“…The predicted downstream effects of these mutations are likely to alter S. 'fitti' metabolism and physiology (Tables S7-S10; Kmiec et al, 2016;Zhang et al, 2018). Subsequently, these changes may enable S. 'fitti' to adapt to the unique metabolic and nutritional demands imposed by each host's microenvironment (Figures 2-5; Tables S7-S10; Muscatine et al, 1989;Reich et al, 2020;Sogin et al, 2014).…”

Genotypic similarity among algal symbionts corresponds to associations with closely related coral hosts

“…Similarly, the candidate genes under selection identified by BayeScan and PCAdapt may underlie the strain differentiation by host species (Tables S7-10). Nonsynonymous mutations in putative cytosolic oligopeptidase and alpha-agarase regions may result in the subtle alteration of zinc and calcium ion binding, respectively, which in turn likely contribute to variation in the physiological capacity of S. 'fitti' (Table S7-S10; Kmiec, Teixeira, Murcha, & Glaser 2016;Zhang et al 2018). Further, these genotypic and phenotypic differences may facilitate the adaptation of each S. 'fitti' strain to the internal and external microenvironments associated with each host niche and meeting their metabolic and nutritional demands (Figs.…”