. Overall Objectives. This project, entitled ?Molecular Mechanisms of Phytochrome Signaling,? (PI J. Clark Lagarias, UC Davis), focuses on gaining fundamental knowledge about the phytochrome family of protein light sensors. Phytochromes utilize linear tetrapyrroles (bilins) as chromophores to sense light quality, quantity and duration. Photochemical light sensing by phytochromes triggers conformational changes that modulate the behavior of living systems via downstream transcriptional cascades. The proposed investigations address the hypothesis that eukaryotic phytochromes share a common signaling mechanism (light-mediated nuclear translocation) despite diverse spectral responses and signaling architectures generated over billions of years of evolution. There are three specific aims focused on 1) conserved protein- chromophore interactions and the interplay between environment and photocycle in plant and algal phytochromes, 2) photoperception and signaling by phytochromes and phytochrome eukaryotic kinases in cryptophyte algae, and 3) intramolecular signal propagation and intermolecular signal transduction by phytochrome in land plants. By examining phytochromes from evolutionarily distant species, our studies seek to elucidate the basis of light sensing and the intramolecular structural changes that are used to control gene expression. To test these hypotheses, we leverage computational analyses to guide experimental design, protein biochemistry and molecular biology to express and purify photoreceptors, enzymology and spectroscopy to understand light-induced changes in photoreceptor structure, forward and reverse genetics for in vivo assessment of nuclear translocation and function in the model land plant Arabidopsis thaliana. Significance. Studies on phytochromes provide fundamental knowledge about how living systems regulate their behavior in response to the external environment. Phytochromes are key regulators for seed germination, seedling establishment, vegetative development and flowering (sexual development). Because of their role in shade sensing, phytochromes are an important limiting factor for yield at high crop densities in modern agriculture. Application of the insights from our studies can improve nutrition, enhance health, lengthen life, and reduce the burdens of illness and disability. Moreover, photosensory proteins are valuable tools for studying function and localization of mammalian proteins (optogenetics), and this work yields new tools for fundamental research on cellular processes of biomedical relevance.

Public Health Relevance

. Nutrition is critical in maintaining human health, and molecular approaches for enhancing agricultural efficiency will play a central role in meeting the demand for food in the face of climate change and increasing human population. A major limitation in improving agriculture is the shade avoidance response caused by competition for light among neighboring plants, which is mediated by phytochrome photoreceptors. This project studies plant and algal phytochromes to learn how phytochromes detect specific colors of light and how they transmit that information to the cell, with the ultimate goal of engineering such responses in crop plants.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function B Study Section (MSFB)
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Barski, Oleg
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University of California Davis
Anatomy/Cell Biology
Schools of Medicine
United States
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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
Rockwell, Nathan C; Lagarias, J Clark; Bhattacharya, Debashish (2014) Primary endosymbiosis and the evolution of light and oxygen sensing in photosynthetic eukaryotes. Front Ecol Evol 2:

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