Identification of small signaling peptide-encoding genes modulated by host and nonhost bacterial pathogens in Arabidopsis

Small signaling peptides (SSPs) play a crucial role in various plant biological processes. However, the involvement of SSPs in plant immunity, particularly during host and nonhost bacterial infection, remains largely unexplored. We established a pipeline using transcriptomics and genetic experimental validation and identified 243 up-regulated and 194 down-regulated SSP-encoding genes upon host and nonhost bacterial pathogen inoculation in Arabidopsis. Four novel up-regulated SSPs with previously uncharacterized roles in plant immunity were experimentally validated, including a defensin-like small cysteine-rich secreted peptide termed S-LOCUS CYSTEINE-RICH LIKE 7 (SCRL7), A DOMAIN of UNKNOWN FUNCTION 538 (DUF538) and two dirigent-like SSPs, named DIR20 and DIR25. Based on the disease phenotypes of mutants and upon synthetic peptide treatments, we determined that SCRL7 plays a negative role while DUF and DIR peptides have a positive role in plant immunity. We established an efficient pipeline to discover pathogen responsive SSPs that could play an important role in plant immunity. This method can also be applied to identify SSPs in other plant physiological processes. These findings contribute to a better understanding of the role of SSPs mediating plant pathogen responses and pave the way for developing new strategies to enhance disease resistance in agriculturally important crops.