Simultaneous profiling of phosphorylation and S-nitrosylation during maize seed germination
Ontology highlight
ABSTRACT:
ORGANISM(S): Zea Mays
SUBMITTER: 
Shijuan Yan
PROVIDER: PXD073327 | iProX | Wed Jan 21 00:00:00 GMT 2026
REPOSITORIES: iProX
Similar Datasets
Project description:Purpose: To identify the potential genes that regulate seed germination speed in maize, we performed a time-series transcriptome analysis with two inbred maize lines (72-3 fast germination, F9721 slow germination) during the seed germination and compared the differentially expressed genes (DEGs) in transcriptome with genes identified by GWAS Methods: Methods: mRNA profiles of two maize inbred lines 72-3 and F9721 showing divergent seed germination at six stages during germination were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed at the gene level. Hisat2 was used to align clean reads to maize B73 reference genome, and HTSeq was used to count transcript abundance. DESeq2 models were used to compare DEGs at each germination stage within or between samples Results: Comparative transcriptome study identified 12 hours after imbibition (HAI) as the critical stage responsible for the variation of germination speed. The DEGs between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways Conclusions: Combined with evidence from gene expression data, GWAS, and gene synteny with other model species, we finally anchored three genes as the likely candidate genes regulating germination speed in maize
2022-03-02 | GSE193292 | GEO
Project description:Rapid and uniform seed germination is required for modern cropping system. Thus, it is important to optimize germination performance through breeding strategies in maize, in which identification for key regulators is needed. Here, we characterized an AP2/ERF transcription factor, ZmEREB92, as a negative regulator of seed germination in maize. Enhanced germination in ereb92 mutants is contributed by elevated ethylene signaling and starch degradation. Consistently, an ethylene signaling gene ZmEIL7 and an α-amylase gene ZmAMYa2 are identified as direct targets repressed by ZmEREB92. OsERF74, the rice ortholog of ZmEREB92, shows conserved function in negatively regulating seed germination in rice. Importantly, this orthologous gene pair is likely experienced convergently selection during maize and rice domestication. Besides, mutation of ZmEREB92 and OsERF74 both lead to enhanced germination under cold condition, suggesting their regulation on seed germination might be coupled with temperature sensitivity. Collectively, our findings uncovered the ZmEREB92-mediated regulatory mechanism of seed germination in maize and provide breeding targets for maize and rice to optimize seed germination performance towards changing climates.
2023-11-09 | GSE234833 | GEO
Project description:Seed germination is a critical developmental process in plant propagation. Knowledge of the gene expression patterns in this critical process is important in order to understand the main biochemical reactions involved in successful germination, specially for economically relevant plants such as Maize. The purpose of this study is the gene expression analysis of quiescent and germinated maize embryonic axes to determine the regulatory mechanism for (r)-protein expression during the maize development process.
2011-08-01 | GSE27648 | GEO
Project description:Yeast protein microarrays were utilized to investigate determinants of S-nitrosylation by biologically relevant low-mass S-nitrosothiols (SNOs). Large numbers of S-nitrosylated yeast proteins were identified after treatment with SNOs, among which those with active-site Cys thiols residing at N termini of alpha-helices or within catalytic loops were particularly prominent. However, S-nitrosylation varied substantially even within these families of proteins (e.g., papain-related Cys-dependent hydrolases and rhodanese/Cdc25 phosphatases), suggesting that neither secondary structure nor intrinsic nucleophilicity of Cys thiols was sufficient to explain specificity. Further analyses revealed a substantial influence of NO-donor stereochemistry and structure on efficiency of S-nitrosylation as well as an unanticipated and important role for allosteric effectors. Thus, high-throughput screening and unbiased proteome coverage reveal multifactorial determinants of S-nitrosylation (which may be overlooked in alternative proteomic analyses), and support the idea that target specificity can be achieved through rational design of S-nitrosothiols Invitrogen yeast Protoarrays for kinase substrate identification (KSI) were treated with S-nitrosothiols and assayed for protein S-nitrosylation by using a modified biotin switch protocol. Slides were scanned and with a Genepix 4000b scanner (Molecular Devices) using Genepix Pro and analyzed by using Prospector Analyzer (Invitrogen). Results were validated using yeast cell lysates and recombinant, purified yeast proteins.
2010-05-19 | E-GEOD-19218 | biostudies-arrayexpress
Project description:Identification of the potential genes regulating seed germination speed in maize
| PRJNA795680 | ENA
Project description:Seed germination is a critical developmental process in plant propagation. Knowledge of the gene expression patterns in this critical process is important in order to understand the main biochemical reactions involved in successful germination, specially for economically relevant plants such as Maize. The purpose of this study is the gene expression analysis of quiescent and germinated maize embryonic axes to determine the regulatory mechanism for (r)-protein expression during the maize development process. This study analyzed samples of total and polysomal RNA from maize embryonic axes at different time periods during the germination process and under the influence of a specific growth factor. For each condition a biological replicate was included and for the time periods, a technical replicate was also included.
2011-07-31 | E-GEOD-27648 | biostudies-arrayexpress
Project description:In this study, Three sRNA libraries were generated and sequenced from embryos treated with GA, ABA and ddH2O (CK). A total of 247 miRNAs (69 known and 178 novel ones) were identified and found that 28 known and 70 novel miRNAs were differentially expressed in embryos with different treatments. Using bioinformatics tool, we predict target genes of the differentially expressed miRNAs. GO enrichment and KEGG pathway analysis for these targets showed that miRNAs differentially expressed in the samples are involved in peroxisome, ribosome and plant hormonal signalling. This study not only improves our knowledge about the roles of miRNAs in maize seed germination but also reveals the potential role of miRNAs in the hormonal responses of different pytohormones.
2018-11-14 | GSE122477 | GEO
Project description:In this study, a small RNA library from maize seed 24 hours after imbibition was sequenced by the Solexa technology. A total of 11,338,273 reads were obtained. 1,047,447 total reads representing 431 unique sRNAs matched to known maize miRNAs. Further analysis confirmed the authenticity of 115 known miRNAs belonging to 24 miRNA families and the discovery of 167 novel miRNAs in maize. Both the known and the novel miRNAs were confirmed by sequencing of a second small RNA library constructed the same way as the one used in the first sequencing. We also found 10 miRNAs that had not been reported in maize, but had been reported in other plant species. All novel sequences had not been earlier described in other plant species. In addition, seven miRNA* sequences were also obtained. Putative targets for 106 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in maize imbibed seed. This study led to the confirmation of the authenticity of 115 known miRNAs and the discovery of 167 novel miRNAs in maize. Identification of novel miRNAs resulted in significant enrichment of the repertoire of maize miRNAs and provided insights into miRNA regulation of genes expressed in imbibed seed.
2014-03-03 | GSE27664 | GEO
Project description:Mycorrhizal fungi colonize orchid seed and induce the germination. This so-called symbiotic germination is a critical developmental process in the lifecycle of all orchids. However, the molecular changes taking place during the orchid seed symbiotic germination still remains largely unknown. To better understand the molecular mechanism of orchid seed germination, we performed comparative transcriptomic and proteomic analysis on Chinese traditional medicinal orchid plants, Dendrobium officinale to explore protein expression change at the different developmental stages between asymbiotic and symbiotic germination and identify the key proteins regulated symbiotic germination of orchid seeds. iTRAQ analysis from 8 samples identified 2256 plant proteins, of which, 308 proteins were differentially expressed across three developmental stages within asymbiotic or symbiotic accession and 229 proteins are differentially expressed in the symbiotic germination compared to asymbiotic germination. 32 proteins are co-upregulated in both proteomic and transcriptomic level for symbiotic germination compared to asymbiotic germination. Our results revealed that symbiotic germination of D. officinale seeds probably shares the common signal pathway with asymbiotic germination during the early germination stage.
2017-05-12 | PXD006102 | Pride
Project description:Yeast protein microarrays were utilized to investigate determinants of S-nitrosylation by biologically relevant low-mass S-nitrosothiols (SNOs). Large numbers of S-nitrosylated yeast proteins were identified after treatment with SNOs, among which those with active-site Cys thiols residing at N termini of alpha-helices or within catalytic loops were particularly prominent. However, S-nitrosylation varied substantially even within these families of proteins (e.g., papain-related Cys-dependent hydrolases and rhodanese/Cdc25 phosphatases), suggesting that neither secondary structure nor intrinsic nucleophilicity of Cys thiols was sufficient to explain specificity. Further analyses revealed a substantial influence of NO-donor stereochemistry and structure on efficiency of S-nitrosylation as well as an unanticipated and important role for allosteric effectors. Thus, high-throughput screening and unbiased proteome coverage reveal multifactorial determinants of S-nitrosylation (which may be overlooked in alternative proteomic analyses), and support the idea that target specificity can be achieved through rational design of S-nitrosothiols
2009-12-01 | GSE19218 | GEO