We are interested in understanding the molecular mechanism by which light regulates gene expression in plants. Our research program is focused on the phytochromes, the major and best-characterized family of plant regulatory photoreceptors. The photoreceptor molecule functions as a biological switch that, upon perception of the light signal, triggers changes in transcription which are detectable within 5 minutes of the stimulus.
The general strategy we have adopted toward this problem is fourfold: (a) to examine the phytochrome molecule for clues to its photosensory function and mechanism of action using structural analysis, phytochrome-defective mutants and overexpression of mutagenized phytochromes in transgenic Arabidopsis; (b) to study genes under phytochrome control to identify promoter DNA elements and transcription factors involved in induction or repression of expression; (c) to identify signal transduction pathway components between the photoreceptor and the genes it regulates using forward and reverse genetic screens for signaling-defective mutants, and molecular interaction screens for phytochrome-interacting proteins; and (d) to dissect the primary transcriptional networks that orchestrate the expression of downstream genes responsible for elaborating light-regulated development, using RNA-seq and ChIP-seq analysis.
Our data suggest: (a) That the phytochromes signal directly to photoresponsive genes by light induced translocation from the cytoplasm into the nucleus, followed by specific physical interaction with promoter-bound transcriptuion factors of the basic helix-loop-helix (bHLH) class; ,(b) That this interaction triggers rapid phosphorylation, ubiquitination and degradation of the transcription factors, using protein kinases and E3 ligases that we have identified, and (c) That genes encoding a master-set of diverse transcriptional regulators, that orchestrate downstream expression in the transcriptional network, are direct targets of this signaling pathway.
We have also exploited the unique features of the phytochrome system to develop a novel light-switchable gene promoter system that is potentially usable in any light-accessible eukaryotic cell system for rapid, conditional induction or repression of expression, a strategy since dubbed "Optogenetics".