John Momo, Khushbu Islam, Souparna Biswas, Abdul Rawoof, Ilyas Ahmad, Vishesh, Nirala Ramchiary
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The mass spectrometry analysis identified a total of 4,473 and 2,012 proteins from the pericarp and placenta tissues of <i>Capsicum</i> fruits. We observed expression of developmental stage-specific proteins, such as kinases, transferases, ion transporters, F-box proteins, and transcription factors that were enriched in the biosynthesis of primary and secondary metabolites. The abundance of these proteins corresponded with RNAseq data. Key proteins related to capsaicinoids biosynthesis, such as Acyltransferase 3, 3-oxoacyl-[acyl-carrier protein], 4-coumaroyl co-A ligase, and 3-ketoacyl-coA synthase 3, were identified in placenta of highly pungent ghost chili, along with J-domain proteins and transcription factors such as MYB101, MYB 14-like, bHLH112, NAC, and Cyt p450 CYP82D47, suggesting their role in capsaicinoids and secondary metabolites biosynthesis. Further, we observed a correlation of the expression of genes and proteins with the abundance of primary and secondary metabolites, such as carbohydrates, alcohols, fatty acids, phenolics, glycerides, polyamines, and amino acids. Our findings provide a novel multiomics resources for future functional studies, with potential applications in breeding programs.</p><p><strong>Graphical abstract: </strong></p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s12298-025-01581-7.</p>","PeriodicalId":20148,"journal":{"name":"Physiology and Molecular Biology of Plants","volume":"31 3","pages":"453-475"},"PeriodicalIF":3.3000,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12006620/pdf/","citationCount":"0","resultStr":"{\"title\":\"Multi-omics analysis of non-pungent (<i>Capsicum annuum</i>) and fiery hot ghost chili (<i>C. chinense</i>) provides insights into proteins involved in fruit development and metabolites biosynthesis.\",\"authors\":\"John Momo, Khushbu Islam, Souparna Biswas, Abdul Rawoof, Ilyas Ahmad, Vishesh, Nirala Ramchiary\",\"doi\":\"10.1007/s12298-025-01581-7\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Global omics offer extensive insights into the diversity of essential biomolecules across various plant developmental stages. Despite advancements in high-throughput technologies, the integrated analysis of global omics such as proteomics, transcriptomics, and metabolomics, is yet to be fully explored in fruits of <i>Capsicum</i> species. In this study, we used an integrated omics approach to identify proteins involved in fruit development, and metabolite biosynthesis in the placenta and pericarp tissues of two contrasting genotypes belonging to ghost chili (<i>Capsicum chinense</i>) and <i>C. annuum</i>. The mass spectrometry analysis identified a total of 4,473 and 2,012 proteins from the pericarp and placenta tissues of <i>Capsicum</i> fruits. We observed expression of developmental stage-specific proteins, such as kinases, transferases, ion transporters, F-box proteins, and transcription factors that were enriched in the biosynthesis of primary and secondary metabolites. The abundance of these proteins corresponded with RNAseq data. Key proteins related to capsaicinoids biosynthesis, such as Acyltransferase 3, 3-oxoacyl-[acyl-carrier protein], 4-coumaroyl co-A ligase, and 3-ketoacyl-coA synthase 3, were identified in placenta of highly pungent ghost chili, along with J-domain proteins and transcription factors such as MYB101, MYB 14-like, bHLH112, NAC, and Cyt p450 CYP82D47, suggesting their role in capsaicinoids and secondary metabolites biosynthesis. Further, we observed a correlation of the expression of genes and proteins with the abundance of primary and secondary metabolites, such as carbohydrates, alcohols, fatty acids, phenolics, glycerides, polyamines, and amino acids. 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Multi-omics analysis of non-pungent (Capsicum annuum) and fiery hot ghost chili (C. chinense) provides insights into proteins involved in fruit development and metabolites biosynthesis.
Global omics offer extensive insights into the diversity of essential biomolecules across various plant developmental stages. Despite advancements in high-throughput technologies, the integrated analysis of global omics such as proteomics, transcriptomics, and metabolomics, is yet to be fully explored in fruits of Capsicum species. In this study, we used an integrated omics approach to identify proteins involved in fruit development, and metabolite biosynthesis in the placenta and pericarp tissues of two contrasting genotypes belonging to ghost chili (Capsicum chinense) and C. annuum. The mass spectrometry analysis identified a total of 4,473 and 2,012 proteins from the pericarp and placenta tissues of Capsicum fruits. We observed expression of developmental stage-specific proteins, such as kinases, transferases, ion transporters, F-box proteins, and transcription factors that were enriched in the biosynthesis of primary and secondary metabolites. The abundance of these proteins corresponded with RNAseq data. Key proteins related to capsaicinoids biosynthesis, such as Acyltransferase 3, 3-oxoacyl-[acyl-carrier protein], 4-coumaroyl co-A ligase, and 3-ketoacyl-coA synthase 3, were identified in placenta of highly pungent ghost chili, along with J-domain proteins and transcription factors such as MYB101, MYB 14-like, bHLH112, NAC, and Cyt p450 CYP82D47, suggesting their role in capsaicinoids and secondary metabolites biosynthesis. Further, we observed a correlation of the expression of genes and proteins with the abundance of primary and secondary metabolites, such as carbohydrates, alcohols, fatty acids, phenolics, glycerides, polyamines, and amino acids. Our findings provide a novel multiomics resources for future functional studies, with potential applications in breeding programs.
Graphical abstract:
Supplementary information: The online version contains supplementary material available at 10.1007/s12298-025-01581-7.
期刊介绍：
Founded in 1995, Physiology and Molecular Biology of Plants (PMBP) is a peer reviewed monthly journal co-published by Springer Nature. It contains research and review articles, short communications, commentaries, book reviews etc., in all areas of functional plant biology including, but not limited to plant physiology, biochemistry, molecular genetics, molecular pathology, biophysics, cell and molecular biology, genetics, genomics and bioinformatics. Its integrated and interdisciplinary approach reflects the global growth trajectories in functional plant biology, attracting authors/editors/reviewers from over 98 countries.
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