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 triggers conformational changes that modulate the behavior of living systems via target molecules that regulate downstream transcriptional cascades. The proposed investigations address the hypothesis that the fundamental mechanism of light sensing has remained conserved throughout billions of years of evolution since endosymbiotic capture of a cyanobacterium by a eukaryotic host. There are three specific aims focused on conservation of photoconversion and protein-chromophore interactions in plant and cyanobacterial phytochromes, the evolutionary genesis of plant phytochrome, and phytochrome photoconversion and signaling activity in land plants. By examining phytochromes from evolutionarily distant species ranging from cyanobacteria to plants, our studies seek to elucidate the basis of light sensing and the intramolecular structural changes that are used to control gene expression. Phytochromes from the glaucophyte Cyanophora paradoxa, the chlorophyte Micromonas pusilla, and the land plants Arabidopsis thaliana and Triticum aestivum (wheat), will be used to examine the hypothesis that light-regulated conformational change triggers translocation to the nucleus in all extant eukaryotic phytochromes. 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, and 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 triggering seed germination, initiating early development of the seedling, and inducing 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, enhancing health, lengthening life, and reducing 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 into such systems.

Public Health Relevance

Phytochromes are an important protein family for human nutrition because of their adverse impact on plant crop yield via their detection of far-red enriched shade in high-density crop plantings, yet our understanding of how phytochromes work in plants remains limited. Our studies will redress this problem by examining the light sensing and signaling output mechanisms of phytochromes from a broad range of species. An understanding of the molecular mechanisms of phytochrome signaling in plants is important wherever inadequate crop yields and opportunistic diseases accompanying malnutrition are responsible for significant human mortality.

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
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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