Project description:The resurrection plant Ramonda serbica Panc. survives long desiccation periods and fully recovers metabolic functions within one day upon watering. This study aimed to identify key candidates and pathways involved in desiccation tolerance in R. serbica. We combined differential transcriptomics and proteomics, phenolic and sugar analysis, FTIR analysis of the cell wall polymers, and detailed analysis of the photosynthetic electron transport (PET) chain. The proteomic analysis allowed the relative quantification of 1192 different protein groups, of which 408 were differentially abundant between hydrated (HL) and desiccated leaves (DL). Almost all differentially abundant proteins related to photosynthetic processes were less abundant, while chlorophyll fluorescence measurements implied shifting from linear PET to cyclic electron transport (CET). The levels of H2O2 scavenging enzymes, ascorbate-glutathione cycle components, catalases, peroxiredoxins, Fe-, and Mn superoxide dismutase (SOD) were reduced in DL. However, six germin-like proteins (GLPs), four Cu/ZnSOD isoforms, three polyphenol oxidases, and 22 late embryogenesis abundant proteins (LEAPs; mainly LEA4 and dehydrins), were desiccation-inducible. Desiccation provoked cell wall remodeling related to GLP-derived H2O2/HO● activity and pectin demethylesterification. This comprehensive study contributes to understanding the role and regulation of the main metabolic pathways during desiccation aiming at crop drought tolerance improvement.
Project description:Co-expression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting the functional roles of individual genes at a system-wide scale. To enable network reconstructions we built a large-scale gene expression atlas comprised of 62,547 mRNAs, 17,862 non-modified proteins, and 6,227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. There was little edge conservation in co-expression and GRNs reconstructed using transcriptome versus proteome data yet networks from either data type were enriched in ontological categories and effective in predicting known regulatory relationships. This integrated gene expression atlas provides a valuable community resource. The networks should facilitate plant biology research and they provide a conceptual framework for future systems biology studies highlighting the importance of studying gene regulation at several levels.
Project description:Co-expression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting the functional roles of individual genes at a system-wide scale. To enable network reconstructions we built a large-scale gene expression atlas comprised of 62,547 mRNAs, 17,862 non-modified proteins, and 6,227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. There was little edge conservation in co-expression and GRNs reconstructed using transcriptome versus proteome data yet networks from either data type were enriched in ontological categories and effective in predicting known regulatory relationships. This integrated gene expression atlas provides a valuable community resource. The networks should facilitate plant biology research and they provide a conceptual framework for future systems biology studies highlighting the importance of studying gene regulation at several levels.
