Genetic analysis of phytochrome signaling in plants and bacteria

A network of receptors and signal-transduction pathways mediate plant responses to changing light environments. The best-characterized components are the phytochrome photoreceptors that regulate plant photomorphogenesis and growth. My thesis explored the genesis of holo-phytochromes and the biological functions of the resulting chromoproteins, using genetics and genomics.; I characterized the first committed step in phytochrome-chromophore biosynthesis starting with an analysis of the Arabidopsis thaliana HY1 locus. hy1 mutants fail to make the phytochrome-chromophore phytochromobilin. I identified HY1 and found that it encodes one member of a heme oxygenase (HO) gene family. To understand the physiological roles of AtHO2, I isolated a ho2 mutation and characterized its phenotypes. Like hy1, ho2-1 was defective in several phytochrome-regulated processes, suggesting that phytochromobilin is limiting in ho2-1. HY1 and AtHO2 are actively expressed in an overlapping pattern. These collective results show that the HY1 and AtHO2 proteins have distinct, but overlapping roles in regulating photomorphogenesis mediated through the genesis of phytochromobilin.; Sequence comparisons of the A. thaliana HOs revealed that this class of enzymes is evolutionarily distant from those present in animals, cyanobacteria, and algae. To obtain insights into common features of plant HOs, I characterized several plant HOs. The derived proteins are similar to each other, but are distantly related to HOs from other organisms. I also demonstrated that the tomato LeHO1 is altered in the yellow-green-2 mutant.; Phytochromes were thought to be unique to photosynthetic organisms. However, I found that these receptors are also present within nonphotosynthetic eubacteria. The encoded proteins contain a chromophore-binding domain attached to a histidine-kinase domain, suggesting that each functions as a light-sensing protein kinase. I have termed this class of prokaryotic photoreceptors the bacteriophytochromes. The Deinococcus radiodurans bacteriophytochrome can form a covalent linkage with bilins to yield a light absorbing chromoprotein. Genetic analysis of the D. radiodurans bacteriophytochrome showed that it functions in a light-sensing pathway to up-regulate carotenoid biosynthesis for protection against intense light. Given their similarity to phytochromes, the bacteriophytochromes should provide a useful paradigm for studying the mechanism(s) of phytochrome action, as they offer a simplified phytochrome-like response in organisms naturally devoid of photosynthesis.