The non-conventional peptidome of Arabidopsis flower development

Unraveling the complexities of genomic data has revealed that the protein coding capacity of eukaryotic genomes has been underestimated. Eukaryotic genomes contain numerous unannotated short open reading frames (sORFs) that, localized in different types of RNA molecules, including long non-coding RNAs, may encode and produce biologically functional peptides. This study focuses on the characterization of the Arabidopsis (Arabidopsis thaliana) sORF-derived flower peptidome, using the floral homeotic mutants apetala1, apetala2, apetala3, pistillata, and agamous in comparison to the wild type. For peptide identification by mass spectrometry (MS), we created an extensive database of hypothetical Arabidopsis peptides, which comprised putative sORF-encoded peptides from intergenic regions, untranslated regions, "non-coding" RNAs and other transcripts. In total, 1,874 hypothetical peptides were detected by MS, of which 132 were selected as higher-confidence peptides for further studies. Sixty of these higher-confidence peptides were predicted to be specifically expressed, or at least enriched, in particular floral organs. Approximately 25% of them belonged to putative gene families in A. thaliana, and 103 had potential homologs in other plant species. Additionally, distinct gene expression patterns were observed, in many cases consisting of specific expression in stamens during flower development.