Transcriptome profiles of etiolated cotyledons exposed to ABA during seedling deetiolation.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1142581 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30058400_1.fastq.gz | Fastqsanger.gz | |||
| SRR30058400_2.fastq.gz | Fastqsanger.gz | |||
| SRR30058401_1.fastq.gz | Fastqsanger.gz | |||
| SRR30058401_2.fastq.gz | Fastqsanger.gz | |||
| SRR30058402_1.fastq.gz | Fastqsanger.gz |
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Project description:The protein crop Lupinus albus stores large amounts of protein in the cotyledons. During epigeal germination the cotyledons emerge from the ground and become photosynthetically active. Proteome and metabolite profiles of the cotyledons demonstrate that (nitrogen) resource allocation from the cotyledons to the developing plant is able to fully support growth on nutrient-poor soils for a prolonged period of time/at least two weeks after germination and thus provides the opportunity to establish specialized structures such as root nodules required for the symbiosis with nitrogen fixing rhizobia and cluster roots improving phosphate uptake.
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Project description:Driven by cell elongation, hypocotyl growth is tightly controlled by light and responds to both external stimuli and endogenous hormonal pathways. Hypocotyls are responsive to the stress signalling hormone abscisic acid (ABA), which effectively inhibits cell elongation. However, how this regulation is connected to light signalling has been a subject of limited studies. Here, we show that, contrary to light-grown seedlings, hypocotyl elongation of dark-grown seedlings is ABA-insensitive. In the dark, hypocotyl sensitivity to ABA is restored in the constitutive photomorphogenic pifq and cop1-4 mutants, suggesting that an active light signalling pathway is necessary for hypocotyl responsiveness to ABA. Surprisingly, etiolated hypocotyls retain an intact ABA signalling pathway, as could be detected by the induction of ABI1 and RD29B transcripts in response to exogenous ABA, suggesting that inhibition of hypocotyl elongation occurs through a divergent path that can be inhibited by PIFs. Here, using RNA-seq analysis we identified a number of ABA differentially expressed genes (DEGs) that correlate with ABA inhibition of hypocotyl elongation. Among these DEGs a number of SMALL AUXIN-UP RNA (SAUR) genes that are known to directly repress D-CLADE TYPE 2C PROTEIN PHOSPHATASES (PP2C.D) were found. The abrogation of PP2CD.D2-SAUR interaction in the pp2c.d2/PP2C.D2M331K -GFP line, restored ABA sensitivity in the dark, suggesting that SAUR proteins, upregulated by PIFs, are sufficient to render hypocotyls insensitive to ABA. This hypocotyl-specific mechanism enables to promote growth towards the light at all costs, overriding ABA inhibition of cell elongation, to ensure subsequent seedling establishment and survival.
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Project description:Background The soybean (Glycine max) cotyledon is a specialized tissue whose main function is to serve as a nutrient reserve that supplies the needs of the young plant throughout seedling development. During this process the cotyledons experience a functional transition to a mainly photosynthetic tissue. To identify at the genetic level the specific active elements that participate in the natural transition of the cotyledon from storage to photosynthetic activity, we studied the transcript abundance profile at different time points using a new soybean oligonucleotide chip containing 19,200 probes (70-mer long). Results After normalization and statistical analysis we determined that 3,594 genes presented a statistically significant altered expression in relation to the imbibed seed in at least one of the time points defined for the study. Detailed analysis of this data identified individual, specific elements of the glyoxylate pathway that play a fundamental role during the functional transition of the cotyledon from nutrient storage to photosynthesis. The dynamics between glyoxysomes and peroxisomes is evident during these series of events. We also identified several other genes whose products could participate co-ordinately throughout the functional transition and the associated mechanisms of control and regulation and we described multiple unknown genetic elements that by association have the potential to make a major contribution to this biological process. Conclusions We demonstrate that the global transcript profile of the soybean cotyledon during seedling development is extremely active, highly regulated and dynamic. We defined the expression profiles of individual gene family members, enzymatic isoforms and protein subunits and classified them accordingly to their involvement in different functional activities relevant to seedling development and the cotyledonary functional transition in soybean, especially the ones associated with the glyoxylate cycle. Our data suggests that in the soybean cotyledon a very complex and synchronized system of control and regulation of several metabolic pathways is essential to carry out the necessary functions during this developmental process. Keywords: Time Course
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Project description:Landscape of RNA NAD+ capping in Arabidopsis seedling with ABA treatment
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