Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation.

MicroProteins are class of small single-domain proteins that post-translationally regulate larger multidomain proteins from which they evolved or to which they relate. They disrupt the normal function of their targets by forming microProtein-target heterodimers through compatible protein-protein interaction (PPI) domains. Recent studies confirm the significance of microProteins in the fine-tuning of plant developmental processes such as shoot apical meristem maintenance and flowering time regulation. While there are a number of well-characterised microProteins in Arabidopsis thaliana, studies from more complex plant genomes are still missing. Our lab has previously developed miPFinder, a software for identifying microProteins from annotated genomes. Here we present an improved version, where we have updated the algorithm to increase its accuracy and speed, and used it to analyse five cereal crop genomes - wheat, rice, barley, maize and sorghum. We found 20,064 potential microProteins from a total of 258,029 proteins in these five organisms, of which approximately 2000 are high-confidence, i.e. likely to function as actual microProteins. Gene ontology analysis of these 2000 microProtein candidates revealed their roles in stress, light and growth responses, hormone signalling and transcriptional regulation. Using a recently developed rice gene co-expression database, we analysed 347 potential rice microProteins that are also conserved in other cereal crops and found over 50 of these rice microProteins co-regulated with their identified interaction partners. Overall, our study reveals a rich source of biotechnologically interesting small proteins that regulate fundamental plant processes such a growth and stress response that could be utilised in crop bioengineering.