Gene Expression Profiling Reveals Defined Functions of the ATP-Binding Cassette Transporter COMATOSE Late in Phase II of Germination

Abstract

Phase II of germination represents a key developmental stage of plant growth during which imbibed seeds either enter stage III of germination, completing the germination process via radicle protrusion, or remain dormant. In this study, we analyzed the influence of the peroxisomal ATP-binding cassette transporter COMATOSE (CTS) on the postimbibition seed transcriptome of Arabidopsis (Arabidopsis thaliana) and also investigated interactions between gibberellin (GA) and CTS function. A novel method for analysis of transcriptome datasets allowed visualization of developmental signatures of seeds, showing that cts-1 retains the capacity to after ripen, indicating a germination block late in phase II. Expression of the key GA biosynthetic genes GA3ox1 and 2 was greatly reduced in cts seeds and genetic analysis suggested that CTS was epistatic to RGL2, a germinationrepressing DELLA protein that is degraded by GA. Comparative analysis of seed transcriptome datasets indicated that specific cohorts of genes were influenced by GA and CTS. CTS function was required for expression of the flavonoid biosynthetic pathway. Confocal imaging demonstrated the exclusive accumulation of flavonoids in the epidermis of wild-type seeds. In contrast, flavonoids were absent from cts and kat2-1 mutant seeds, but accumulated following the application of sucrose, indicating an essential role for b-oxidation in inducing flavonoid biosynthetic genes. These results demonstrate that CTS functions very late in phase II of germination and that its function is required for the expression of specific gene sets related to an important biochemical pathway associated with seedling establishment and survival.

Karrikins enhance light responses during germination and seedling development in Arabidopsis thaliana

“…To determine whether KAR 1 induces similar transcriptional effects as other treatments influencing germination, we performed multiple comparisons to previously published microarray datasets examining light-, dormancy-, and hormone-responsive genes (14,(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39). These results are summarized in Table S3 and S4, and the most striking findings are discussed here.…”

The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis

“…In the absence of activity of the ABI3 or ABI5 transcription factors, PRT6 function is not required because ABA sensitivity is removed. RGL2 is one member of the DELLA family of proteins that has been shown to negatively regulate germination (24,31). Removal of RGL2 activity is required for activation of GA-regulated responses (24,32).…”

Induction of Dormancy in Arabidopsis Summer Annuals Requires Parallel Regulation of DOG1 and Hormone Metabolism by Low Temperature and CBF Transcription Factors

“…There is little overlap between the two data sets. (D) Analysis of differentially regulated genes by TAGGIT (Carrera et al, 2007). For description of overrepresented gene ontologies, see main text.…”

“…Genes involved in ABA signaling in general showed an increase in expression at the warmer temperature, although these changes were in general only twofold or less and are expected to be much less important than the large difference in CYP707A2 expression and the magnitude of the effect of ABA on their protein levels. Finally, to identify groups of genes regulated by seed maturation temperatures, we used the TAGGIT ontology (Carrera et al, 2007) to compare gene expression between the two data sets ( Figure 1D). In the dormant low-temperature-set seeds, cell wall modification, heat shock, and protein degradation were the most prominent categories, whereas in the low dormant seeds, translation, photosynthesis, seed storage proteins, and ethylene were better represented.…”