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. 2008 May;147(1):143-55.
doi: 10.1104/pp.107.110841. Epub 2008 Mar 21.

Elucidating the germination transcriptional program using small molecules

George W Bassel  1 , Pauline Fung, Tsz-fung Freeman Chow, Justin A Foong, Nicholas J Provart, Sean R Cutler
Affiliations

Elucidating the germination transcriptional program using small molecules

George W Bassel et al. Plant Physiol. 2008 May.

Abstract

The transition from seed to seedling is mediated by germination, a complex process that starts with imbibition and completes with radicle emergence. To gain insight into the transcriptional program mediating germination, previous studies have compared the transcript profiles of dry, dormant, and germinating after-ripened Arabidopsis (Arabidopsis thaliana) seeds. While informative, these approaches did not distinguish the transcriptional responses due to imbibition, shifts in metabolism, or breaking of dormancy from those triggered by the initiation of germination. In this study, three mechanistically distinct small molecules that inhibit Arabidopsis seed germination (methotrexate, 2, 4-dinitrophenol, and cycloheximide) were identified using a small-molecule screen and used to probe the germination transcriptome. Germination-responsive transcripts were defined as those with significantly altered transcript abundance across all inhibitory treatments with respect to control germinating seeds, using data from ATH1 microarrays. This analysis identified numerous germination regulators as germination responsive, including the DELLA proteins GAI, RGA, and RGL3, the abscisic acid-insensitive proteins ABI4, ABI5, ABI8, and FRY1, and the gibberellin receptor GID1A. To help visualize these and other publicly available seed microarray data, we designed a seed mRNA expression browser using the electronic Fluorescent Pictograph platform. An overall decrease in gene expression and a 5-fold greater number of transcripts identified as statistically down-regulated in drug-inhibited seeds point to a role for mRNA degradation or turnover during seed germination. The genes identified in our study as responsive to germination define potential uncharacterized regulators of this process and provide a refined transcriptional signature for germinating Arabidopsis seeds.

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Figures

Figure 1.
Figure 1.
Seed eFP browser output. eFP output is illustrated using ABI2 (At5g57050) as an example. Transcript abundance is high in dry seeds of both Col and Cvi accessions. These transcripts rapidly decline by 3 HAI in Col seeds, whereas a low level of expression is maintained in dormant Cvi seeds. The TAGGIT button belonging to the ABA category is highlighted at the bottom with a red box, indicating ABI2 is a part of this group of genes.
Figure 2.
Figure 2.
ABA TAGGIT ontology. TAGGIT ontology categories showing expression data for these genes across all seed microarray experiments are shown. The ABI2 gene is highlighted with a red box. Hierarchical clustering of expression data is represented by the tree to the right, and the curved lines demonstrate confirmed and predicted protein-protein interactions (Geisler-Lee et al., 2007).
Figure 3.
Figure 3.
Overlap of drug-defined transcript profiles and prior germination data. Proportional Venn diagrams illustrating overlap between previously described germination signatures (Carrera et al., 2007) and gene expression in ABA-inhibited seeds are shown. A, Venn diagram showing genes up-regulated in germinating Ler and Cvi seeds in relation to the GermUP dataset. B, Genes up-regulated in dormant Ler and Cvi seeds compared with the GermDOWN dataset. C, GermDOWN and ABAUP gene sets as determined using the SAM method. D, GermUP and ABADOWN gene sets.
Figure 4.
Figure 4.
Drug-specific transcriptional responses. Effect of the individual drug treatments on gene expression in Arabidopsis seeds is shown. Gene sets were defined as genes up- or down-regulated 2-fold or more by each of the treatments relative the control. A, Up-regulated genes in each of the three drugs. B, Genes down-regulated.
Figure 5.
Figure 5.
Photosynthetic nuclear-encoded transcript responses in germinating seeds. Transcript abundance of genes encoding the protein components of photosynthesis in wild-type and various mutant Arabidopsis seeds during germination are shown. Log2-transformed data are relative to the mean of all seed samples in the BAR, with red indicating transcript abundance above the mean and blue indicating abundance below the mean. Arabidopsis mutants were freshly harvested from their mother plants and placed to germinate on agar-water for 24 h (Carrera et al., 2008). Heat maps were generated at the BAR (www.bar.utoronto.ca).
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References

    1. Alboresi A, Gestin C, Leydecker MT, Bedu M, Meyer C, Truong HN (2005) Nitrate, a signal relieving seed dormancy in Arabidopsis. Plant Cell Environ 28 500–512 - PubMed
    1. Armstrong JI, Yuan S, Dale JM, Tanner VN, Theologis A (2004) Identification of inhibitors of auxin transcriptional activation by means of chemical genetics in Arabidopsis. Proc Natl Acad Sci USA 101 14978–14983 - PMC - PubMed
    1. Bentsink L, Jowett J, Hanhart CJ, Koornneef M (2006) Cloning of DOG1, a quantitative trait locus controlling seed dormancy in Arabidopsis. Proc Natl Acad Sci USA 103 17042–17047 - PMC - PubMed
    1. Bewley JD (1997) Breaking down the walls—a role for endo-beta-mannanase in release from seed dormancy? Trends Plant Sci 2 464–469
    1. Bewley JD, Black M (1994) Seeds: Physiology of Development and Germination, Ed 2. Plenum Press, New York

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