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United States Department of Agriculture

Agricultural Research Service

Title: Mutant Screen Distinguishes between Residues Necessary for Light-Signal Perception and Signal Transfer by Phytochrome B

item Oka, Yoshito
item Matsushita, Tomonao
item Mochizuki, Nobuyoshi
item Quail, Peter
item Nagatani, Akira

Submitted to: PLoS Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/10/2008
Publication Date: 8/15/2008
Publication URL:;jsessionid=C2098E5CFE7F898E20B4E27BEC0EBEDF?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1000158&representation=PDF
Citation: Oka, Y., Matsushita, T., Mochizuki, N., Quail, P.H., Nagatani, A. 2008. Mutant Screen Distinguishes between Residues Necessary for Light-Signal Perception and Signal Transfer by Phytochrome B. PLoS Genet. 4(8):e1000158. doi:10.1371/journal.pgen.1000158.

Interpretive Summary: Adapting to the light environment, plants have evolved several photoreceptors, of which the phytochromes are specialized in perceiving the red and far-red light region of the spectrum. Although phytochrome was first discovered in plants, the phytochrome species are present in several organisms, including bacteria. The mechanisms by which phytochromes transduce light signals to downstream components are most well studied in plants. Upon light activation, phytochromes translocate from the cytoplasm into nucleus and regulate the gene expression network through interaction with nuclear transcription factors. The phytochrome molecule can be divided into two major domains: the N-terminal moiety, which is responsible for the light perception, and the C-terminal moiety. Although the C-terminal moiety was thought to be involved in signal transduction, it has recently been shown that the N-terminal moiety has a role not only in light perception, but also in light signal transfer to the downstream network. However, no signaling motifs have been found in the N-terminal moiety. In this study, we analyzed intragenic mutations derived from a genetic screen and found a cluster of residues necessary for signal transduction in a small region neighboring the light-sensing chromophore moiety on the three-dimensional structure. This is an important step towards understanding how a major plant photoreceptor, phytochrome, intramolecularly processes the light signal to trigger diverse physiological responses.

Technical Abstract: The phytochromes (phyA to phyE) are a major plant photoreceptor family that regulate a diversity of developmental processes in response to light. The N-terminal 651–amino acid domain of phyB (N651), which binds an open tetrapyrrole chromophore, acts to perceive and transduce regulatory light signals in the cell nucleus. The N651 domain comprises several subdomains: the N-terminal extension, the Per/Arnt/Sim (PAS)-like subdomain (PLD), the cGMP phosphodiesterase/adenyl cyclase/FhlA (GAF) subdomain, and the phytochrome (PHY) subdomain. To define functional roles for these subdomains, we mutagenized an Arabidopsis thaliana line expressing N651 fused in tandem to green fluorescent protein, ß-glucuronidase, and a nuclear localization signal. A large-scale screen for long hypocotyl mutants identified 14 novel intragenic missense mutations in the N651 moiety. These new mutations, along with eight previously identified mutations, were distributed throughout N651, indicating that each subdomain has an important function. In vitro analysis of the spectral properties of these mutants enabled them to be classified into two principal classes: light-signal perception mutants (those with defective spectral activity), and signaling mutants (those normal in light perception but defective in intracellular signal transfer). Most spectral mutants were found in the GAF and PHY subdomains. On the other hand, the signaling mutants tend to be located in the N-terminal extension and PLD. These observations indicate that the N-terminal extension and PLD are mainly involved in signal transfer, but that the C-terminal GAF and PHY subdomains are responsible for light perception. Among the signaling mutants, R110Q, G111D, G112D, and R325K were particularly interesting. Alignment with the recently described three-dimensional structure of the PAS-GAF domain of a bacterial phytochrome suggests that these four mutations reside in the vicinity of the phytochrome light-sensing knot.

Last Modified: 06/24/2017
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