Phytochromes are biliprotein photosensors that coordinate gene expression, and growth and development of plants. They optimize light harvesting when light is limiting, and minimize light damage when light is too intense. The widespread occurrence of phytochromes in eubacteria and fungi demonstrates that these sensors are also important for adapation by heterotrophic organisms to the circadian light environment. We seek to define how light signals are perceived by phytochromes and transduced to target molecules. Our investigations address the hypothesis that bilin photoisomerization induces a 'counterion-switch'within the photoreceptor which alters ATP-dependent protein-protein interactions and phosphotransferase activities for both prokaryotic (cyanobacterial) and eukaryotic (plant) phytochrome models. These studies will use a combination of computational approaches, i.e. quantum calculations, homology modeling and molecular dynamics simulations, chemi-enzymatic synthesis of linear chromophore analogs, biochemistry and molecular biology for mutagenesis and isolation of photoreceptors with various chromophores, fluorescence, calorimetry and single-molecule assays to probe ATP- and light-modulated protein-protein interactions, together with spectroscopic analysis of wild type and phytochrome mutants in vitro. Companion experiments exploit our discovery of a fluorescent, constitutively activated allele for in vivo dissection of phytochrome signaling using a combination of fluorescence microscopy techniques and suppressor mutagenesis in the genetic model Arabidopsis thaliana. Phytochromes are important regulatory targets, not only for minimizing plant crop yield losses to far-red enriched shade and reflected light, but also for design of drugs that target both pathogenic and beneficial microorganisms. An understanding of the molecular mechanisms of phytochrome signaling in plants is of particular significance to the developing world where inadequate crop yields and opportunistic diseases accompanying malnutrition are responsible for significant human mortality. While mammals lack this family of light sensors, phytochrome studies have already provided valuable insight into common mechanisms of cell signaling important to cancer and diabetes.
| Kirpich, Julia S; Mix, L Tyler; Martin, Shelley S et al. (2018) Protonation Heterogeneity Modulates the Ultrafast Photocycle Initiation Dynamics of Phytochrome Cph1. J Phys Chem Lett 9:3454-3462 |
| Baloban, Mikhail; Shcherbakova, Daria M; Pletnev, Sergei et al. (2017) Designing brighter near-infrared fluorescent proteins: insights from structural and biochemical studies. Chem Sci 8:4546-4557 |
| Rockwell, Nathan C; Lagarias, J Clark (2017) Phytochrome diversification in cyanobacteria and eukaryotic algae. Curr Opin Plant Biol 37:87-93 |
| Wittkopp, Tyler M; Schmollinger, Stefan; Saroussi, Shai et al. (2017) Bilin-Dependent Photoacclimation in Chlamydomonas reinhardtii. Plant Cell 29:2711-2726 |
| Duanmu, Deqiang; Rockwell, Nathan C; Lagarias, J Clark (2017) Algal light sensing and photoacclimation in aquatic environments. Plant Cell Environ 40:2558-2570 |
| Rockwell, Nathan C; Martin, Shelley S; Li, Fay-Wei et al. (2017) The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2. New Phytol 214:1145-1157 |
| Rockwell, Nathan C; Lagarias, J Clark (2017) Ferredoxin-dependent bilin reductases in eukaryotic algae: Ubiquity and diversity. J Plant Physiol 217:57-67 |
| Berlin, Shai; Carroll, Elizabeth C; Newman, Zachary L et al. (2015) Photoactivatable genetically encoded calcium indicators for targeted neuronal imaging. Nat Methods 12:852-8 |
| Jones, Matthew Alan; Hu, Wei; Litthauer, Suzanne et al. (2015) A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light. Plant Physiol 169:814-25 |
| Kim, Peter W; Rockwell, Nathan C; Martin, Shelley S et al. (2014) Heterogeneous photodynamics of the pfr state in the cyanobacterial phytochrome Cph1. Biochemistry 53:4601-11 |
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