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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM068552-09
Application #
8440083
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Anderson, Vernon
Project Start
2003-08-05
Project End
2016-11-30
Budget Start
2013-01-01
Budget End
2013-11-30
Support Year
9
Fiscal Year
2013
Total Cost
$325,456
Indirect Cost
$105,456
Name
University of California Davis
Department
Anatomy/Cell Biology
Type
Schools of Medicine
DUNS #
047120084
City
Davis
State
CA
Country
United States
Zip Code
95618
Duanmu, Deqiang; Bachy, Charles; Sudek, Sebastian et al. (2014) Marine algae and land plants share conserved phytochrome signaling systems. Proc Natl Acad Sci U S A 111:15827-32
Chen, Andrew; Li, Chengxia; Hu, Wei et al. (2014) Phytochrome C plays a major role in the acceleration of wheat flowering under long-day photoperiod. Proc Natl Acad Sci U S A 111:10037-44
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
Kim, Peter W; Rockwell, Nathan C; Martin, Shelley S et al. (2014) Dynamic inhomogeneity in the photodynamics of cyanobacterial phytochrome Cph1. Biochemistry 53:2818-26
Rockwell, Nathan C; Duanmu, Deqiang; Martin, Shelley S et al. (2014) Eukaryotic algal phytochromes span the visible spectrum. Proc Natl Acad Sci U S A 111:3871-6
Kim, Peter W; Rockwell, Nathan C; Freer, Lucy H et al. (2013) Unraveling the Primary Isomerization Dynamics in Cyanobacterial Phytochrome Cph1 with Multi-pulse Manipulations. J Phys Chem Lett 4:2605-2609
Hu, Wei; Franklin, Keara A; Sharrock, Robert A et al. (2013) Unanticipated regulatory roles for Arabidopsis phytochromes revealed by null mutant analysis. Proc Natl Acad Sci U S A 110:1542-7
Kim, Peter W; Freer, Lucy H; Rockwell, Nathan C et al. (2012) Second-chance forward isomerization dynamics of the red/green cyanobacteriochrome NpR6012g4 from Nostoc punctiforme. J Am Chem Soc 134:130-3
Rockwell, Nathan C; Martin, Shelley S; Feoktistova, Kateryna et al. (2011) Diverse two-cysteine photocycles in phytochromes and cyanobacteriochromes. Proc Natl Acad Sci U S A 108:11854-9
Song, Ji-Young; Cho, Hye Sun; Cho, Jung-Il et al. (2011) Near-UV cyanobacteriochrome signaling system elicits negative phototaxis in the cyanobacterium Synechocystis sp. PCC 6803. Proc Natl Acad Sci U S A 108:10780-5

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