Peptidome and Transcriptome Analysis of Plant Peptides Involved in Bipolaris maydis Infection of Maize

Identification of peptidome-based biomarkers of cassava mosaic disease resistance in different cassava varieties

Cassava, a major economic crop in Thailand, yielded over 3 million USD in exports in 2023. However, its production has been declining since 2021 due to cassava mosaic disease (CMD) outbreaks, which affect cassava plantations. CMD infections have recently increased due to the scarcity of healthy stems and CMD-resistant varieties, the latter being key to controlling its spread. Developing novel methods is critical for accelerating the cultivation of high-yield, CMD-resistant varieties. In this study, signature peptide patterns were determined using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-tandem MS (LC-MS/MS) to screen for CMD-resistant varieties. Peptide mass fingerprint (PMF) analyses revealed distinct peptide barcodes across 11 varieties, clearly delineating CMD-resistant and CMD-tolerant phenotypes. LC-MS/MS and orthogonal partial least squares-discriminant analysis (OPLS-DA) further demonstrated clear distinctions between the peptide profiles of different phenotypes. Heatmap and PMF analyses consistently revealed unique peptide patterns across the varieties. Volcano plot analysis identified seven upregulated peptides-TATTVAGS, PAAGGGGG, PNELLSYSE, SSIEEGGS, GGGVGGPL, NNGGGFSV, and GPGPAPAA-in CMD-resistant plants. These peptides were associated with proteins containing CONSTANS-like zinc finger, C2H2-type, GST N-terminal, Tubby-like F-box, nuclear-localized AT-hook motif, auxin response factor, and C2 domains. Altogether, this study identified peptidome-based biomarkers for screening CMD-resistant varieties; however, further validation using larger samples is necessary.

Navigating the landscape of plant proteomics

In plants, proteins are fundamental to virtually all biological processes, such as photosynthesis, signal transduction, metabolic regulation, and stress responses. Studying protein distribution, function, modifications, and interactions at the cellular and tissue levels is critical for unraveling the complexities of these biological pathways. Protein abundance and localization are highly dynamic and vary widely across the proteome, presenting a challenge for global protein quantification and analysis. Mass spectrometry-based proteomics approaches have proven to be powerful tools for addressing this complex issue. In this review, we summarize recent advancements in proteomics research and their applications in plant biology, with an emphasis on the current state and challenges of studying post-translational modifications, single-cell proteomics, and protein-protein interactions. Additionally, we discuss future prospects for plant proteomics, highlighting potential opportunities that proteomics technologies offer in advancing plant biology research.

Transfer of pesticides and metabolites in corn: Production, processing, and livestock dietary burden

Corn stover is widely used in livestock feed but has received limited attention regarding its potential risks. In this study, pesticide residues were monitored across 12 provinces in China, and terminal residues of four pesticides, chlorantraniliprole, thiamethoxam, epoxiconazole, and pyraclostrobin, were tested. In addition, the silage processing experiment was conducted. All processing factors (PF) were <1, indicating pesticide degradation. The physicochemical properties of pesticides, especially log P, were related to degradation efficiency. Pesticides with higher log P values showed higher PFs (0.43 to 0.85), indicating lower degradation efficiency. The dietary burden of livestock before and after silage processing was calculated using OECD livestock dietary burden calculator. Results showed that after silage fermentation, the dietary burden was reduced by 28.8 % to 79.2 %. Throughout the entire production and processing process, the fastest degradation of all pesticides in whole corn was primarily observed from the pesticide application time to the harvest time, with some pesticides also showing accelerated degradation during subsequent processing stages. Therefore, in actual production, especially for pesticides which are difficult to degrade, appropriate extension of the safety interval or selection of suitable processing methods can be taken to further reduce pesticide residues in agricultural products.

Current Challenges and Future Directions in Peptidomics

The field of peptidomics has been under development since its start more than 20 years ago. In this chapter we provide a personal outlook for future directions in this field. The applications of peptidomics technologies are spreading more and more from classical research of peptide hormones and neuropeptides towards commercial applications in plant and food-science. Many clinical applications have been developed to analyze the complexity of biofluids, which are being addressed with new instrumentation, automization, and data processing. Additionally, the newly developed field of immunopeptidomics is showing promise for cancer therapies. In conclusion, peptidomics will continue delivering important information in classical fields like neuropeptides and peptide hormones, benefiting from improvements in state-of-the-art technologies. Moreover, new directions of research such as immunopeptidomics will further complement classical omics technologies and may become routine clinical procedures. Taken together, discoveries of new substances, networks, and applications of peptides can be expected in different disciplines.