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Karrikins control seedling photomorphogenesis through the HY5-BBX transcriptional module.

ABSTRACT: Karrikins (KARs) are a class of butenolide molecules found in the smoke of burned plant material that can induce germination of many plant species that emerge after fire. Intriguingly, KAR perception is widely conserved and not limited to fire-followers. For example, germination of dormant Arabidopsis thaliana seeds can also be stimulated by KARs. Additionally, KAR treatment enhances responses of seedlings to light. These responses include inhibition of hypocotyl elongation, enhancement of cotyledon expansion, and transcriptional upregulation of light-responsive genes not only in Arabidopsis but also in Brassica tournefortii. Although the core KAR signaling mechanism, consisting of KAI2-SCF/MAX2-mediated degradation of SMAX1 and SMXL2, is well described, it remains elusive how SMXL degradation leads to downstream growth responses. In this study, we analyse the role of BBX20 in the KAR signaling pathway through both chemical and genetic approaches using knock-out mutants. We find that BBX20, together with its close homologue BBX21, is essential for KAR-induced inhibition of hypocotyl elongation and anthocyanin accumulation. Our detailed genetic analysis suggests that BBX20 and BBX21 act in a HY5-dependent transcriptional module downstream of SMAX1 and SMXL2. While RNA-seq analysis revealed large-scale transcriptional changes in the smax1 smxl2 mutant, our results clearly suggest that BBX20 and BBX21 are required for a subset of SMAX1/SMXL2-dependent transcriptional regulation. Overall, our data suggest that the KAR signaling pathway promotes the activity of the HY5-BBX transcriptional module and that this module represents a point of convergence between KAR and light signaling.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE166857 | GEO | 2021/09/06

REPOSITORIES: GEO

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Project description:LONG HYPOCOTYL 5 (HY5) is a basic leucine zipper transcription factor (TF) that functions downstream of multiple families of photoreceptors. Mutations in the HY5 gene cause a myriad of aberrant phenotypes in Arabidopsis, including elongated hypocotyl, reduced accumulation of pigments, halted chloroplast development in greening hypocotyls, altered root morphology and defective hormonal and stimulus responses. HY5 thus acts as an integrater that links various gene networks to coordinate plant development. Here we report an effort to experimentally map the HY5-mediated gene networks in Arabidopsis by integrating genomic loci occupied by HY5 and HY5-dependent gene expression profiles. Our results indicate HY5 binds to over 9,000 genes, which detectably impact the expression of over 1,100 genes, either positively or negatively. Further, HY5 indirectly regulates many other genes through sub-networks mediated by other regulators. In particular, we show that HY5 regulates eight microRNA (miRNA) genes, which in turn control transcript abundance of specific target genes. Over-expressing the HY5-targeted miR408 resulted in phenotypes that are opposite to hy5 mutants. Together our results revealed both the transcriptional and post-transcriptional components of the HY5-mediated gene networks responsible for the phenotypic complexity in plants. DNase I-treated total RNA was prepared from wild type and hy5-215 seedlings grown under wild type light (WL). The mRNA fraction was extracted from total RNA using Dynabeads oligo(dT)25 (Invitrogen) following the manufacturerM-bM-^@M-^Ys directions. First- and second-strand cDNA were generated usingSuperScript II and random hexamer primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the manufacturerM-bM-^@M-^Ys protocol (Illumina). Bowtie (Langmead et al., 2009) was used to map the sequence reads to the Arabidopsis genome and only uniquely mapped reads were used in subsequent analyses.

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Karrikins control seedling photomorphogenesis through the HY5-BBX transcriptional module.

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