Defining the full spectrum of mechanisms used by eukaryotic cells to perceive, transduce and respond to extracellular signals remains a central goal of contemporary biomedical research. The program here is focused on the mechanisms by which cells track and respond to informational light signals from the environment. Perception of such signals by the cytoplasmically-localized, phytochrome (phy) photosensory receptors initiates a transduction process that culminates in the altered expression of nuclear genes that direct an array of morphogenic responses. The long-term goal of this research is to define the molecular mechanisms by which this process occurs. Current evidence indicates that a small subfamily of bHLH transcription factors, termed PIFs (for phy-Interacting Factors), promote skotomorphogenic development in darkness, and that this activity is reversed by direct binding of photoactivated phy molecules, following their light-induced translocation into the nucleus. Signal transfer in this process involves phy-induced phosphorylation, ubiquitylation and degradation of the PIFs, with consequent transcriptional changes that drive a transition to photomorphogenic development. Despite recent progress, the mechanistic bases of the molecular and biochemical transactions at the phy-PIF and PIF-genome interfaces remain to be fully defined.
The specific aims of this A1 proposal are: (A) To define the molecular and biochemical mechanisms underlying signaling at the phy-PIF interface, focused on the coupled activities of newly-identified protein kinases and ubiquitin ligases, that are recruited, with PIF3 by activated phyB (a pseudokinase), into a multiprotein complex, that concomitantly transduces and attenuates light signals to direct-target genes (DTGs). (B) To define the mechanistic basis of a newly identified bimodal regulation of PIF transcriptional activation of DTGs, involving both differential between-PIF promoter occupancy and quantitative local modulation of the intrinsic activity of DNA-bound PIFs. A multi-track strategy will be used involving mass-spectrometry, yeast 1-, 2- and 3-hybrid, and protein-microarray screens to identify candidate interactors in phy-PIF signaling complexes and/or molecular-modifiers of bound-PIF transcriptional activity, coupled with reverse-genetic assessment of the in vivo functional relevance of such candidates;in vitro biochemical reconstitution experiments will be used to dissect the activities within the signaling complex;a DNA-affinity-purification-sequencing (DAP-seq) procedure will be used to define sequences responsible for target-promoter selectivity among the PIFs;and epigenome maps of the PIF-DTG promoters will be generated to examine the role of PIF-chromatin interactions in regulating differential PIF transcriptional activity.

Public Health Relevance

Understanding the full array of molecular and cellular mechanisms by which cells perceive and transduce external signals remains an important goal of the biomedical sciences. Disruption of cellular signaling circuitry is a major cause of human diseases, such as cancer. The research proposed here will probe the mechanisms by which identified molecules involved in two facets of signaling, known to cause human cancer, work in the cell. Definition of such mechanisms has the potential to provide targets for drug treatments.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Cellular Signaling and Regulatory Systems Study Section (CSRS)
Program Officer
Maas, Stefan
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Berkeley
Other Basic Sciences
Schools of Earth Sciences/Natur
United States
Zip Code
Ni, Weimin; Xu, Shou-Ling; González-Grandío, Eduardo et al. (2017) PPKs mediate direct signal transfer from phytochrome photoreceptors to transcription factor PIF3. Nat Commun 8:15236
Dalton, Jutta C; Bätz, Ulrike; Liu, Jason et al. (2016) A Modified Reverse One-Hybrid Screen Identifies Transcriptional Activation Domains in PHYTOCHROME-INTERACTING FACTOR 3. Front Plant Sci 7:881
Martín, Guiomar; Leivar, Pablo; Ludevid, Dolores et al. (2016) Phytochrome and retrograde signalling pathways converge to antagonistically regulate a light-induced transcriptional network. Nat Commun 7:11431
Soy, Judit; Leivar, Pablo; González-Schain, Nahuel et al. (2016) Molecular convergence of clock and photosensory pathways through PIF3-TOC1 interaction and co-occupancy of target promoters. Proc Natl Acad Sci U S A 113:4870-5
Cordeiro, André M; Figueiredo, Duarte D; Tepperman, James et al. (2016) Rice phytochrome-interacting factor protein OsPIF14 represses OsDREB1B gene expression through an extended N-box and interacts preferentially with the active form of phytochrome B. Biochim Biophys Acta 1859:393-404
Martínez-García, Jaime F; Gallemí, Marçal; Molina-Contreras, María José et al. (2014) The shade avoidance syndrome in Arabidopsis: the antagonistic role of phytochrome a and B differentiates vegetation proximity and canopy shade. PLoS One 9:e109275
Ni, Weimin; Xu, Shou-Ling; Tepperman, James M et al. (2014) A mutually assured destruction mechanism attenuates light signaling in Arabidopsis. Science 344:1160-1164
Pfeiffer, Anne; Shi, Hui; Tepperman, James M et al. (2014) Combinatorial complexity in a transcriptionally centered signaling hub in Arabidopsis. Mol Plant 7:1598-1618
Ni, Weimin; Xu, Shou-Ling; Chalkley, Robert J et al. (2013) Multisite light-induced phosphorylation of the transcription factor PIF3 is necessary for both its rapid degradation and concomitant negative feedback modulation of photoreceptor phyB levels in Arabidopsis. Plant Cell 25:2679-98
Zhang, Yu; Mayba, Oleg; Pfeiffer, Anne et al. (2013) A quartet of PIF bHLH factors provides a transcriptionally centered signaling hub that regulates seedling morphogenesis through differential expression-patterning of shared target genes in Arabidopsis. PLoS Genet 9:e1003244

Showing the most recent 10 out of 67 publications