Genome-Wide Identification and Characterization of Small Peptides in Maize

Abstract

Small peptides (sPeptides), <100 amino acids (aa) long, are encoded by small open reading frames (sORFs) often found in the 5′ and 3′ untranslated regions (or other parts) of mRNAs, in long non-coding RNAs, or transcripts from introns and intergenic regions; various sPeptides play important roles in multiple biological processes. In this study, we conducted a comprehensive study of maize (Zea mays) sPeptides using mRNA sequencing, ribosome profiling (Ribo-seq), and mass spectrometry (MS) on six tissues (each with at least two replicates). To identify maize sORFs and sPeptides from these data, we set up a robust bioinformatics pipeline and performed a genome-wide scan. This scan uncovered 9,388 sORFs encoding peptides of 2–100 aa. These sORFs showed distinct genomic features, such as different Kozak region sequences, higher specificity of translation, and high translational efficiency, compared with the canonical protein-coding genes. Furthermore, the MS data verified 2,695 sPeptides. These sPeptides perfectly discriminated all the tissues and were highly associated with their parental genes. Interestingly, the parental genes of sPeptides were significantly enriched in multiple functional gene ontology terms related to abiotic stress and development, suggesting the potential roles of sPeptides in the regulation of their parental genes. Overall, this study lays out the guidelines for genome-wide scans of sORFs and sPeptides in plants by integrating Ribo-seq and MS data and provides a more comprehensive resource of functional sPeptides in maize and gives a new perspective on the complex biological systems of plants.

RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints

“…We also compared RiboNT, RiboTaper and RiboCode, which have been widely applied in the identification of sORFs in varied species including several plants [ 34 ], for the identification of experimentally verified sORFs. For this test, Baker’s yeast ( S. cerevisiae ) provided an ideal genome dataset, in which the sORFs had been experimentally validated by labelling with detectable tags (GFP or HA) [ 1 , 4 ].…”

The Small Open Reading Frame‐Encoded Peptides: Advances in Methodologies and Functional Studies

“…Very recently, the application of PRICE has contributed to the identification of 525 noncanonical immunopeptides that are derived from sORFs [60] . Apart from PRICE, RibORF and RiboCode have also been applied to reference database construction for mining SEPs from MS data [21,61] …”

“…[60] Apart from PRICE, RibORF and RiboCode have also been applied to reference database construction for mining SEPs from MS data. [21,61] However, it is almost unlikely to eliminate the translationirrelevant binding between ribosome and transcripts in Riboseq, and thus the probability of false discovery is increased. [62] In addition, the difference of algorithm design may lead to fairly different sORF prediction results from the same Ribo-seq data.…”

Inter‐tissue and inter‐organ signaling in drought stress response and phenotyping of drought tolerance

“…Therefore, the functions of these predicted peptide‐encoding genes have to be analyzed. In maize, sORFs and small peptides (sPeptides) were systematically surveyed based on genomic and mass spectrometry data (Liang et al, 2021 ). Based on these systematic analyses, 9338 sORFs 3–300 nucleotides in length and 2695 sPeptides were identified in the maize genome.…”