Application of new genomic methods to the characterization of Arabidopsis thaliana photomorphogenesis

Abstract

The ability of plants to not only detect but also adjust to their environment is crucial for their survival. The genes involved in photomorphogenesis – developmental changes in response to light – and their regulation have long been of interest to researchers. While the phytochrome and cryptochrome photoreceptors have been isolated and partially characterized, the downstream components of the light signaling pathway which transmit the perceived light signals and regulate gene expression are still being discovered. A negative regulator of photomorphogenesis, DET1 (de-etiolated 1), was discovered in a mutant screen for plants that develop a light grown phenotype in the dark. DET1 is nuclear localized, but its exact function remains unknown. Two contrasting mechanisms for the role of DET1 in the regulation of gene expression have been proposed based on studies of the tomato and human orthologs of DET1. In order to reveal the mechanism and molecular context of DET1 action, suppressor mutant screens were employed to discover additional genes acting in conjunction with DET1 (designated as TED genes). In this research, new genomic methods were developed and employed to identify the genes underlying the ted1-1SD and ted2-1D suppressor mutations. A long hypocotyl QTL and suppression of the det1-1 dark grown phenotype by the Bensheim (Be-0) ecotype of Arabidopsis mapped to the HAT4 gene, a homeoboxdomain leucine-zipper transcription factor involved in shade-avoidance responses. Sequence analysis uncovered two functionally distinct alleles of HAT4 in the Be-0 alleles of HAT4 compared to the genomic standard Columbia (Col-0) ecotype. Expression analysis showed that in addition to negative autoregulation by itself, HAT4 is also negatively regulated by DET1. The ted2-1D mutation was mapped to a 57 Kbp interval on chromosome I containing three likely candidate genes. Suppression of the det1-1 phenotype by ted2-1D is overdominant which is highly unusual and typically associated with hybrid vigor or heterosis traits. The discovery of the genes underlying the ted1-1SD and ted2-1D suppressor mutations have furthered the understanding of the role for DET1 in regulation of photomorphogenesis as well as mechanisms involved in overall gene regulation during light signaling.