# Molecular mechanisms of phytochrome signaling

> **NIH NIH R01** · UNIVERSITY OF CALIFORNIA AT DAVIS · 2020 · $356,390

## Abstract

Summary.
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.

## Key facts

- **NIH application ID:** 9837443
- **Project number:** 5R01GM068552-16
- **Recipient organization:** UNIVERSITY OF CALIFORNIA AT DAVIS
- **Principal Investigator:** JOHN CLARK LAGARIAS
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $356,390
- **Award type:** 5
- **Project period:** 2003-08-05 → 2020-12-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/9837443

## Citation

> US National Institutes of Health, RePORTER application 9837443, Molecular mechanisms of phytochrome signaling (5R01GM068552-16). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/9837443. Licensed CC0.

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