Abstract
BackgroundProtein degradation is a basic cell process that operates in general protein turnover or to produce bioactive peptides. However, very little is known about the qualitative and quantitative composition of a plant cell peptidome, the actual result of this degradation. In this study we comprehensively analyzed a plant cell peptidome and systematically analyzed the peptide generation process.ResultsWe thoroughly analyzed native peptide pools of Physcomitrella patens moss in two developmental stages as well as in protoplasts. Peptidomic analysis was supplemented by transcriptional profiling and quantitative analysis of precursor proteins. In total, over 20,000 unique endogenous peptides, ranging in size from 5 to 78 amino acid residues, were identified. We showed that in both the protonema and protoplast states, plastid proteins served as the main source of peptides and that their major fraction formed outside of chloroplasts. However, in general, the composition of peptide pools was very different between these cell types. In gametophores, stress-related proteins, e.g., late embryogenesis abundant proteins, were among the most productive precursors. The Driselase-mediated protonema conversion to protoplasts led to a peptide generation “burst”, with a several-fold increase in the number of components in the latter. Degradation of plastid proteins in protoplasts was accompanied by suppression of photosynthetic activity.ConclusionWe suggest that peptide pools in plant cells are not merely a product of waste protein degradation, but may serve as important functional components for plant metabolism. We assume that the peptide “burst” is a form of biotic stress response that might produce peptides with antimicrobial activity from originally functional proteins. Potential functions of peptides in different developmental stages are discussed.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0468-7) contains supplementary material, which is available to authorized users.
Highlights
Protein degradation is a basic cell process that operates in general protein turnover or to produce bioactive peptides
We found that the two developmental stages of P. patens, namely protonemata and gametophores, as well as protoplasts, contain thousands of endogenous peptides resulting from degradation of functionally active proteins
Peptidome of P. patens protoplasts We suggest several hypotheses to explain the dramatic increase in the numbers of precursor proteins, as well as of protoplast-specific peptides, that occur in the protoplast peptidome: 1) an immune response leading to specific degradation of cell proteins; 2) an increase in protein degradation rate induced by stress; and 3) protein degradation due to programmed cell death (Figure 4)
Summary
Protein degradation is a basic cell process that operates in general protein turnover or to produce bioactive peptides. Degradation of originally functional proteins can contribute to functional peptidomes in eukaryotic organisms [2,12,13,14,15,16,17]. Examples of such peptides in plants are inseptin, which is a fragment of chloroplast ATP synthase from cowpea (Vigna unguiculata) [18], and the GmSubPep and GmPep914 peptides produced from soy (Glycine max) subtilisin-like protease [19,20]. Little is known about the generation of the proteolytic degradome in plant cells and tissues or its physiological role
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