The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms

A substantial but largely unexplored fraction of eukaryotic proteomes is composed of peptides and small proteins (the peptidome). In recent years, short open reading frames (sORFs) capable of encoding functional peptides have been identified within transcripts annotated as non-coding RNAs or in intergenic regions. These sORF-encoded peptides (SEPs) were previously overlooked due to their small size and difficulties in detection, both experimentally and computationally. However, analyses of translating RNAs (ribosome profiling) and proteomics (mass spectrometry) have provided growing evidence for the existence of numerous novel 'non-conventional' peptides in eukaryotic organisms, including plants. In animals, mounting evidence indicates that long non-coding RNAs are an important source of SEPs, and that SEPs participate in crucial cellular and physiological processes and can mediate the evolution of novel characteristics. Similar findings are now emerging in plants. The SEP-coding capacity and the full repertoire of functional SEPs within eukaryotic genomes remain unclear, but systematic, large-scale molecular screenings are beginning to address this gap. Here, we review current progress in understanding the plant non-conventional peptidome, explore parallels between plants and animals, and illustrate how findings in animals can help guide plant research on this topic.