Project description:In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. Three biological replicates for 4-d-old seedlings grown under dark or red-light and long-day (0.5 ?mole m-2 sec-1) contitions.
Project description:In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development. In response to environmental light signals, transcriptomic adjustment plays an important role in Arabidopsis seed germination and seedling development. G-box cis-element is commonly present in promoters of genes positively or negatively responding to the light signal. For the pursuit of additional transcriptional regulator modulating light-mediated transcriptome changes, we have identified AtbZIP16, a basic region/leucine zipper motif transcription factor, via G-box DNA affinity chromatography. We have confirmed that AtbZIP16 possesses G-box-specific binding activity. Analyses of atbzip16 mutants indicate that AtbZIP16 is a negative regulator in phyB-mediated inhibition of cell elongation, but a positive regulator in phytochrome-mediated seed germination process. Transcriptomic analysis supports that AtbZIP16 is primarily a transcriptional repressor regulating light-, GA- and ABA-responsive genes. Chromatin immunoprecipitation study revealed that AtbZIP16 could directly target RGL2, a DELLA gene, and indirectly repress the expression of PIL5 gene, which encodes a bHLH protein inhibiting seed germination in Arabidopsis. Our study indicated that, through repressing the expression of RGL2 and the antagonizing the expression of PIL5, AtbZIP16 functions to promote seed germination and hypocotyl elongation during early stages of Arabidopsis seedling development.
Project description:Arabidopsis seedling were exposed in co-culture to E. amylovora mVOC and data show that mVOCs promote plant growth and early responses
Project description:The developmental program of seed formation and seedling development requires not only tight regulation of cell division and metabolism but also the adaption of organelles in structure and function. Therefore, changes in organellar protein composition is one crucial factor in development. Of particular interest in plants is the switch to photoautotrophic growth, for which biosynthesis and degradation of lipid droplets (LDs) play a critical role. We present here a bottom-up proteomics study analyzing eight different developmental phases during silique development, seed germination and seedling establishment. We investigated both total protein fractions and LD-enriched fractions for each time point. The overall changes in the seed and seedling proteome during germination and seedling establishment monitored in this study present a rich resource for researchers interested in different questions of early seedling biology. The analysis of the proteome of LDs using LD-enrichment factors allowed the identification of four LD-associated protein families, which were subsequently confirmed by a cell biological approach. In addition to protein discovery, our dataset allows for the study of the dynamics of LD proteins throughout the developmental phases analyzed. We found that the relative levels of oleosin stay stable, while many other proteins accumulate on LDs at later stages of seedling establishment. The methodology described here is shown to be well suited for describing a comprehensive and quantitative view of the Arabidopsis proteome across time, with a particular focus on proteins associated with LDs.
Project description:The developmental program of seed formation and seedling development requires not only tight regulation of cell division and metabolism but also the adaption of organelles in structure and function. Therefore, changes in organellar protein composition is one crucial factor in development. Of particular interest in plants is the switch to photoautotrophic growth, for which biosynthesis and degradation of lipid droplets (LDs) play a critical role. We present here a bottom-up proteomics study analyzing eight different developmental phases during silique development, seed germination and seedling establishment. We investigated both total protein fractions and LD-enriched fractions for each time point. The overall changes in the seed and seedling proteome during germination and seedling establishment monitored in this study present a rich resource for researchers interested in different questions of early seedling biology. The analysis of the proteome of LDs using LD-enrichment factors allowed the identification of four LD-associated protein families, which were subsequently confirmed by a cell biological approach. In addition to protein discovery, our dataset allows for the study of the dynamics of LD proteins throughout the developmental phases analyzed. We found that the relative levels of oleosin stay stable, while many other proteins accumulate on LDs at later stages of seedling establishment. The methodology described here is shown to be well suited for describing a comprehensive and quantitative view of the Arabidopsis proteome across time, with a particular focus on proteins associated with LDs.
Project description:We used Ribo-seq (Ribosome profiling) combining with RNA-seq to explore the translational landscape of Arabidopsis Col-0 seedling. We generated 6 biological replicates of RNA-seq and Ribo-seq data for Arabidopsis Col-0 seedling. 3 of the replicates were collected after 20 minutes of 0.1% DMSO treatment and the other 3 samples were collected after 60 minutes of DMSO treatmeant. The resulting RNA-seq and Ribo-seq files were used to discover translated up-stream ORFs (uORFs) and analyze the translation efficiency of uORF-containing genes in Arabidopsis.