Non-conventional peptides (NCPs), which include small open reading frame-encoded peptides, play critical roles in fundamental biological processes. Here we developed an integrated peptidogenomic pipeline using high-throughput mass spectra to probe a customized six-frame translation database and applied it to large-scale identification of NCPs in plants. Altogether, 1,993 and 1,860 NCPs were unambiguously identified in maize and Arabidopsis, respectively. The NCPs showed distinct characteristics compared to conventional peptides (CPs) and were derived from introns, 3'UTRs, 5'UTRs, junctions and intergenic regions. These results revealed that translation events in unannotated transcripts occurred more broadly than previously thought. In addition, maize NCPs were found to be enriched within regions associated with phenotypic variations and domestication selection, indicating their potential function in plant genetic regulations of complex traits and evolution. Summarily, this study provides an unbiased and global view of plant NCPs. The identification of large-scale NCPs in both monocot and dicot plants reveals that a much larger portion of the plant genome can be translated to biologically functional molecules, which has important implications in functional genomic studies. The present study also provides a useful resource for the characterization of more hidden NCPs in other plants.

Nuclear factor-Y (NF-Y) transcription factors are important regulators of several essential biological processes, including embryogenesis, drought resistance, meristem maintenance, and photoperiod-dependent flowering in Arabidopsis. However, the regulatory mechanisms of NF-Ys in maize (Zea mays) are not well understood yet. In this study, we identified an NF-Y transcription factor, ZmNF-YA3. Genome-wide analysis showed that ZmNF-YA3 bound to >6000 sites in the maize genome, 2259 of which are associated with genic sequences. ZmNF-YA3 was found to interact with CONSTANS-like (CO-like) and flowering promoting factor1 (FPF1) through yeast two-hybrid and bimolecular fluorescence complementation (BiFC) assays. Quantitative real-time reverse transcription-PCR (qRT-PCR) combined with yeast one-hybrid assay and EMSA suggested that NF-YA3 could promote early flowering by binding to the FLOWERING LOCUS T-like12 (FT-like12) promoter in maize. Morerover, we also showed that ZmNF-YA3 could improve drought and high-temperature tolerance through binding to the promoter regions of bHLH92, FAMA, and the jasmonic acid activator MYC4, respectively. These results contribute to a comprehensive understanding of the molecular mechanisms and regulatory networks of NF-Y transcription factors in regulating maize flowering time and stress response in maize.

Multidrug-resistant (MDR) bacteria pose a major threat to public health, and additional sources of antibacterial candidates are urgently needed. Noncanonical peptides (NCPs), derived from noncanonical small open reading frames, represent small biological molecules with important roles in biology. However, the antibacterial activity of NCPs remains largely unknown. Here, we discovered a plant-derived noncanonical antibacterial peptide (NCBP1) against both Gram-positive and Gram-negative bacteria. NCBP1 is composed of 11 amino acid residues with cationic surface potential and favorable safety and stability. Mechanistic studies revealed that NCBP1 displayed antibacterial activity by targeting phosphatidylglycerol and cardiolipin in bacterial membrane, resulting in membrane damage and dysfunction. Notably, NCBP1 showed promising efficacy in mice. Furthermore, NCBP1 effectively inhibited the growth of plant fungal pathogens and enhanced disease resistance in maize. Our results demonstrate the unexplored antimicrobial potential of plant-derived NCPs and provide an accessible source for the discovery of antimicrobial substances against MDR bacterial and fungal pathogens.

Summary: Southern corn rust (SCR), which is a destructive disease caused by Puccinia polysora Underw. (P. polysora), commonly occurs in warm‐temperate and tropical regions. To identify candidate proteins related to SCR resistance and characterize the molecular mechanisms underlying the maize–P. polysora interaction, a comparative proteomic analysis of susceptible and resistant maize lines was performed. Statistical analyses revealed 1489 differentially abundant proteins in the resistant line, as well as 1035 differentially abundant proteins in the susceptible line. After the P. polysora infection, the abundance of one remorin protein (ZmREM1.3) increased in the resistant genotype, but decreased in the susceptible genotype. Plant‐specific remorins are important for responses to microbial infections as well as plant signalling processes. In this study, transgenic maize plants overexpressing ZmREM1.3 exhibited enhanced resistance to the biotrophic P. polysora. In contrast, homozygous ZmREM1.3 UniformMu mutant plants were significantly more susceptible to P. polysora than wild‐type plants. Additionally, the ZmREM1.3‐overexpressing plants accumulated more salicylic acid (SA) and jasmonic acid (JA). Moreover, the expression levels of defence‐related genes were higher in ZmREM1.3‐overexpressing maize plants than in non‐transgenic control plants in response to the P. polysora infection. Overall, our results provide evidence that ZmREM1.3 positively regulates maize defences against P. polysora likely via SA/JA‐mediated defence signalling pathways. This study represents the first large‐scale proteomic analysis of the molecular mechanisms underlying the maize–P. polysora interaction. This is also the first report confirming the remorin protein family affects plant resistance to SCR.