Gene Mining for Proline Based Signaling Proteins in Cell Wall of Arabidopsis thaliana

Abstract

The cell wall (CW) as a first line of defense against biotic and abiotic stresses is of primary importance in plant biology. The proteins associated with cell walls play a significant role in determining a plant's sustainability to adverse environmental conditions. In this work, the genes encoding cell wall proteins (CWPs) in Arabidopsis were identified and functionally classified using geneMANIA and GENEVESTIGATOR with published microarrays data. This yielded 1605 genes, out of which 58 genes encoded proline-rich proteins (PRPs) and glycine-rich proteins (GRPs). Here, we have focused on the cellular compartmentalization, biological processes, and molecular functioning of proline-rich CWPs along with their expression at different plant developmental stages. The mined genes were categorized into five classes on the basis of the type of PRPs encoded in the cell wall of Arabidopsis thaliana. We review the domain structure and function of each class of protein, many with respect to the developmental stages of the plant. We have then used networks, hierarchical clustering and correlations to analyze co-expression, co-localization, genetic, and physical interactions and shared protein domains of these PRPs. This has given us further insight into these functionally important CWPs and identified a number of potentially new cell-wall related proteins in A. thaliana.

Proline oxidation fuels mitochondrial respiration during dark-induced leaf senescence in Arabidopsis thaliana

“…Proline could originate from the degradation of cellular and cell wall proteins, which are notably rich in proline and hydroxy (Ihsan et al , 2017), as has also been described for the mammalian extracellular matrix (Pandhare et al , 2009). Degradation of cell wall proteins could therefore lead to an increase of free proline concentration in the cell that would act as an activator of ProDH transcription and as a substrate for both ProDH isoforms, contributing to nitrogen remobilization through glutamine generation from glutamate and its subsequent transport to sinks.…”

A mitochondrial prolyl aminopeptidase PAP2 releases N‐terminal proline and regulates proline homeostasis during stress response

“…Our findings show that pap2 knockouts exhibit an accelerated dark-induced senescence when tested in both detached and attached leaves ( Figure 6). During leaf senescence, proline can be obtained from the degradation of organelle and cell wall proteins, which have high proline and hydroxyproline content (Ihsan et al, 2017). Inactivation of PAP2 combined with the downregulation of mitochondrial amino acid biosynthesis during senescence (Breeze et al, 2011) may further decrease proline abundance and consequently accelerate senescence progression.…”

“…Both PAP1 and PAP2 contain not only the conserved Ser-His-Asp triad, but also conserved features specific to S33 serine peptidase family according to MEROPS classification (Rawlings et al, 2018), including a/b hydrolase folds and three distinct S33 fingerprint motifs (Figure 1c). One of these motifs contains the conserved catalytic serine motif GXSZG, where X and Z represent any amino acid and bulky hydrophobic amino acid, respectively (Ito et al, 2013). In most PAP1 homologues, X and Z are, respectively, substituted by glycine and tryptophan, whereas in most PAP2 homologues, X and Z are represented by glutamine and phenylalanine/tyrosine (Figure 1b).…”

“…Studies in bacteria have shown that a conserved serine residue is essential for PAP catalytic activity (Kitazono et al, 1994a), hence categorised as a S33 serine peptidase in MEROPS. PAP catalytic activity and structure has been most comprehensively described in bacteria, showing specificity against N-terminal proline and hydroxyproline (Ito et al, 2013). Bacterial PAP primarily targets smaller peptides of up to 12 aa long, whereby its activity decreases with longer peptides (Ito et al, 2013).…”

“…PAP catalytic activity and structure has been most comprehensively described in bacteria, showing specificity against N-terminal proline and hydroxyproline (Ito et al, 2013). Bacterial PAP primarily targets smaller peptides of up to 12 aa long, whereby its activity decreases with longer peptides (Ito et al, 2013). Overexpression of an Arabidopsis PAP1 isoform (At2g14260.2) resulted in an increase of accumulated free proline in leaf tissues, and a higher tolerance to drought and high salinity stresses (Sun et al, 2013).…”