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Transcriptome profiling of erf4 seeds in Arabidopsis thaliana

ABSTRACT: Seeds establish dormancy for survival under severe conditions and break it for renascence under suitable ones. Here We identify a fate switch constituted by MKK3-MPK7 and ERF4 responsible for the transition of seeds state from dormancy to germination. We show that the MKK3-MPK7 module is activated by dormancy-breaking factors, affects and relies on the expression of some EXPAs to control seed dormancy. Furthermore, we identify a direct downstream substrate of this module, ERF4, which can suppress the expression of these EXPAs by directly binding to the GCC box in their exon region. The activated MKK3-MPK7 module phosphorylates ERF4 and leads to its rapid degradation, thereby releasing its inhibitory effect on the expression of these EXPAs. Our work identifies a signaling chain integrated by protein phosphorylation, degradation, and gene transcription, dependent on which the germination promoters within the embryonic nucleus are sensing and activated by the germination signals from the ambient conditions.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE230392 | GEO | 2023/04/30

REPOSITORIES: GEO

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Project description:Plant embryos can survive years in a desiccated, quiescent state within seeds. In many species, seeds are dormant and unable to germinate at maturity. They acquire the capacity to germinate through a period of dry storage called after-ripening (AR), a biological process that occurs at 5-15% moisture when most metabolic processes cease. Because stored transcripts will be among the first proteins translated upon water uptake, they likely impact germination potential. Transcriptome changes associated with the increased seed dormancy of the GA-insensitive sly1-2 mutant, and with dormancy loss through sly1-2 after-ripening or constitutive overexpression of the GA receptor (GID1b) were characterized in dry seeds. This experiment used the same seed batches as a previous experiment (E-MTAB-4782) to characterize transcriptional changes associated with the increased seed dormancy and dormancy loss in imbibing seeds. The SLY1 gene encodes the F-box subunit of an SCF E3 ubiquitin ligase needed for GA-triggered proteolysis of DELLA repressors of seed germination. In the sly1-2 mutant, GA-directed DELLA proteolysis cannot occur leading to DELLA protein accumulation and increased dormancy. sly1-2 mutant seeds are fully dormant at 2 weeks of dry storage (0% germination), but germinate well with very long after-ripening (51% germination after 19 months). sly1-2 seed germination can also be rescued by overexpression of the GA receptor, GA-INSENSITIVE DWARF1b (GID1b-OE), which resulted in 74% germination at 2 weeks of dry storage. In this experiment, we sampled dry seeds of wild-type Ler at 2 weeks of dry storage (non-dormant), dormant sly1-2 (2 weeks of dry storage; sly1-2(D)), long after-ripened sly1-2 (non-dormant, 19 months of dry storage; sly1-2(AR)), and sly1-2 GID1b-OE (non-dormant, 2 weeks of dry storage). This experimental design allowed comparison between these transcriptomes in dry seeds to determine if dry seed stored mRNA differences contribute to the dormancy phenotypes observed once seeds are imbibed. Seeds for Ler wt, sly1-2(D), and sly1-2 GID1b-OE were grown alongside each other under the same conditions and after-ripened for 2 weeks. Seeds from sly1-2(AR) were grown under the same conditions in advance of the other lines to allow for the long after-ripening requirement. RNA was extracted using a phenol-chloroform-based extraction from three biological replicates per treatment.

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Transcriptome profiling of erf4 seeds in Arabidopsis thaliana

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