Divergence in red light responses associated with thermal reversion of PHYTOCHROME B between high‐ and low‐latitude species

Phytochrome B (PHYB) triggers diverse light responses in Arabidopsis by binding to a group of antagonistically acting PHYTOCHROME-INTERACTING transcription FACTORs (PIFs) to promote PIF degradation, consequently downregulating PIF target genes. However, whether PHYB directly controls the transactivation activity of PIFs remains ambiguous. Here we show that the prototypic PIF, PIF3, possesses a p53-like transcription activation domain (TAD) consisting of a sequence-specific, hydrophobic activator motif surrounded by acidic residues. A PIF3mTAD mutant in which the activator motif is replaced with alanines fails to activate PIF3 target genes in Arabidopsis in dark, light, and shade conditions, validating the in vivo functions of the PIF3 TAD. Intriguingly, binding of the N-terminal photosensory module of PHYB to the PHYB-binding site adjacent to the TAD inhibits its transactivation activity. These results unveil a photoresponsive transcriptional switching mechanism in which photoactivated PHYB directly masks the transactivation activity of PIF3. Our study also suggests the unexpected conservation of sequence-specific TADs between the animal and plant kingdoms.

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Interactive Effects of Light Quality and Temperature on Arabidopsis Growth and Immunity

Plant and Cell Physiology ◽

10.1093/pcp/pcaa020 ◽

2020 ◽

Vol 61 (5) ◽

pp. 933-941

Author(s):

Xiaoying Liu ◽

Chunmei Xue ◽

Le Kong ◽

Ruining Li ◽

Zhigang Xu ◽

...

Keyword(s):

Disease Resistance ◽

Blue Light ◽

Light Quality ◽

Red Light ◽

Complex Interaction ◽

Hypocotyl Elongation ◽

Interactive Effects ◽

Phytochrome B ◽

Light Conditions ◽

Effects Of Temperature

Abstract We report here the interactive effects of three light qualities (white, red and blue) and three growth temperatures (16�C, 22�C and 28�C) on rosette growth, hypocotyl elongation and disease resistance in Arabidopsis thaliana. While an increase in temperature promotes hypocotyl elongation irrespective of light quality, the effects of temperature on rosette growth and disease resistance are dependent on light quality. Maximum rosette growth rate under white, red and blue light are observed at 28�C, 16�C and 22�C, respectively. The highest disease resistance is observed at 16�C under all three light conditions, but the highest susceptibility is observed at 28�C for white light and 22�C for red and blue light. Interestingly, rosette growth is inhibited by phytochrome B (PHYB) under blue light at 28�C and by cryptochromes (CRYs) under red light at 16�C. In addition, disease resistance is inhibited by PHYB under blue light and promoted by CRYs under red light. Therefore, this study reveals a complex interaction between light and temperature in modulating rosette growth and disease resistance as well as the contribution of PHYB and CRY to disease resistance.

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Light Gradient-Based Screening of Arabidopsis thaliana on a 384-Well Type Plant Array Chip

Micromachines ◽

10.3390/mi11020191 ◽

2020 ◽

Vol 11 (2) ◽

pp. 191

Author(s):

Youn-Hee Park ◽

Je-Kyun Park

Keyword(s):

Arabidopsis Thaliana ◽

White Light ◽

Solid Medium ◽

Red Light ◽

Phytochrome B ◽

Wild Type ◽

Light Gradient ◽

Gradient Based ◽

Light Effects ◽

Germination And Growth

Arabidopsis thaliana (Arabidopsis), as a model for plant research, is widely used for various aspects of plant science. To provide a more sophisticated and microscopic environment for the germination and growth of Arabidopsis, we report a 384-well type plant array chip in which each Arabidopsis seed is independently seeded in a solid medium. The plant array chip is made of a poly(methyl methacrylate) (PMMA) acrylic material and is assembled with a home-made light gradient module to investigate the light effects that significantly affect the germination and growth of Arabidopsis. The light gradient module was used to observe the growth pattern of seedlings according to the intensity of the white light and to efficiently screen for the influence of the white light. To investigate the response to red light (600 nm), which stimulates seed germination, the light gradient module was also applied to the germination test. As a result, the germination results showed that the plant array chip can be used to simultaneously screen wild type seeds and phytochrome B mutant seeds on a single array chip according to the eight red light intensities.

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Arabidopsis chloroplast J protein DJC75/CRRJ mediates nitrate-promoted seed germination in the dark

Annals of Botany ◽

10.1093/aob/mcaa040 ◽

2020 ◽

Vol 125 (7) ◽

pp. 1091-1099

Author(s):

Huai-Syuan Ciou ◽

Yu-Lun Tsai ◽

Chi-Chou Chiu

Keyword(s):

Arabidopsis Thaliana ◽

Seed Germination ◽

Germination Rate ◽

Red Light ◽

Phytochrome B ◽

Biosynthetic Gene ◽

Unknown Mechanism ◽

J Domain ◽

Domain Protein ◽

J Protein

Abstract Background and Aims Nitrate can stimulate seed germination of many plant species in the absence of light; however, the molecular mechanism of nitrate-promoted seed germination in the dark remains largely unclear and no component of this pathway has been identified yet. Here, we show that a plastid J-domain protein, DJC75/CRRJ, in arabidopsis (Arabidopsis thaliana) is important for nitrate-promoted seed germination in the dark. Methods The expression of DJC75 during imbibition in the dark was investigated. The seed germination rate of mutants defective in DJC75 was determined in the presence of nitrate when light cues for seed germination were eliminated by the treatment of imbibed seeds with a pulse of far-red light to inactivate phytochrome B (phyB), or by assaying germination in the dark with seeds harbouring the phyB mutation. The germination rates of mutants defective in CRRL, a J-like protein related to DJC75, and in two chloroplast Hsp70s were also measured in the presence of nitrate in darkness. Key Results DJC75 was expressed during seed imbibition in the absence of light. Mutants defective in DJC75 showed seed germination defects in the presence of nitrate when light cues for seed germination were eliminated. Mutants defective in CRRL and in two chloroplast Hsp70s also exhibited similar seed germination defects. Upregulation of gibberellin biosynthetic gene GA3ox1 expression by nitrate in imbibed phyB mutant seeds was diminished when DJC75 was knocked out. Conclusions Our data suggest that plastid J-domain protein DJC75 regulates nitrate-promoted seed germination in the dark by upregulation of expression of the gibberellin biosynthetic gene GA3ox1 through an unknown mechanism and that DJC75 may work in concert with chloroplast Hsp70s to regulate nitrate-promoted seed germination. DJC75 is the first pathway component identified for nitrate-promoted seed germination in the dark.

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Deconstructing and repurposing the light-regulated interplay between Arabidopsis phytochromes and interacting factors

Communications Biology ◽

10.1038/s42003-019-0687-9 ◽

2019 ◽

Vol 2 (1) ◽

Cited By ~ 4

Author(s):

David Golonka ◽

Patrick Fischbach ◽

Siddhartha G. Jena ◽

Julius R. W. Kleeberg ◽

Lars-Oliver Essen ◽

...

Keyword(s):

Mammalian Cells ◽

Red Light ◽

Interaction Data ◽

Phytochrome B ◽

Adaptive Responses ◽

Membrane Recruitment ◽

C Terminus ◽

Regulated Gene Expression ◽

Insight Into ◽

Differential Affinity

AbstractPhytochrome photoreceptors mediate adaptive responses of plants to red and far-red light. These responses generally entail light-regulated association between phytochromes and other proteins, among them the phytochrome-interacting factors (PIF). The interaction with Arabidopsis thaliana phytochrome B (AtPhyB) localizes to the bipartite APB motif of the A. thaliana PIFs (AtPIF). To address a dearth of quantitative interaction data, we construct and analyze numerous AtPIF3/6 variants. Red-light-activated binding is predominantly mediated by the APB N-terminus, whereas the C-terminus modulates binding and underlies the differential affinity of AtPIF3 and AtPIF6. We identify AtPIF variants of reduced size, monomeric or homodimeric state, and with AtPhyB affinities between 10 and 700 nM. Optogenetically deployed in mammalian cells, the AtPIF variants drive light-regulated gene expression and membrane recruitment, in certain cases reducing basal activity and enhancing regulatory response. Moreover, our results provide hitherto unavailable quantitative insight into the AtPhyB:AtPIF interaction underpinning vital light-dependent responses in plants.

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Response of the photosynthetic apparatus to UV-A and red light in the phytochrome B-deficient Arabidopsis thaliana L. hy3 mutant

Photosynthetica ◽

10.1007/s11099-016-0212-z ◽

2016 ◽

Vol 54 (3) ◽

pp. 321-330 ◽

Cited By ~ 15

Author(s):

V. D. Kreslavski ◽

F. J. Schmitt ◽

C. Keuer ◽

T. Friedrich ◽

G. N. Shirshikova ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Red Light ◽

Photosynthetic Apparatus ◽

Phytochrome B

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On the (un)coupling of the chromophore, tongue interactions, and overall conformation in a bacterial phytochrome

Journal of Biological Chemistry ◽

10.1074/jbc.ra118.001794 ◽

2018 ◽

Vol 293 (21) ◽

pp. 8161-8172 ◽

Cited By ~ 20

Author(s):

Heikki Takala ◽

Heli K. Lehtivuori ◽

Oskar Berntsson ◽

Ashley Hughes ◽

Rahul Nanekar ◽

...

Keyword(s):

Conformational Changes ◽

Structural Changes ◽

Deinococcus Radiodurans ◽

Red Light ◽

Light Responses ◽

Structural Mechanism ◽

Weakly Coupled ◽

Activity State ◽

Conserved Tyrosine

Phytochromes are photoreceptors in plants, fungi, and various microorganisms and cycle between metastable red light–absorbing (Pr) and far-red light–absorbing (Pfr) states. Their light responses are thought to follow a conserved structural mechanism that is triggered by isomerization of the chromophore. Downstream structural changes involve refolding of the so-called tongue extension of the phytochrome-specific GAF-related (PHY) domain of the photoreceptor. The tongue is connected to the chromophore by conserved DIP and PRXSF motifs and a conserved tyrosine, but the role of these residues in signal transduction is not clear. Here, we examine the tongue interactions and their interplay with the chromophore by substituting the conserved tyrosine (Tyr263) in the phytochrome from the extremophile bacterium Deinococcus radiodurans with phenylalanine. Using optical and FTIR spectroscopy, X-ray solution scattering, and crystallography of chromophore-binding domain (CBD) and CBD–PHY fragments, we show that the absence of the Tyr263 hydroxyl destabilizes the β-sheet conformation of the tongue. This allowed the phytochrome to adopt an α-helical tongue conformation regardless of the chromophore state, hence distorting the activity state of the protein. Our crystal structures further revealed that water interactions are missing in the Y263F mutant, correlating with a decrease of the photoconversion yield and underpinning the functional role of Tyr263 in phytochrome conformational changes. We propose a model in which isomerization of the chromophore, refolding of the tongue, and globular conformational changes are represented as weakly coupled equilibria. The results also suggest that the phytochromes have several redundant signaling routes.

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FIN5 Positively Regulates Far-red Light Responses in Arabidopsis thaliana

Plant and Cell Physiology ◽

10.1093/pcp/pcg071 ◽

2003 ◽

Vol 44 (6) ◽

pp. 565-572 ◽

Cited By ~ 2

Author(s):

Dae-Shik Cho ◽

Sung-Hyun Hong ◽

Hong-Gil Nam ◽

Moon-Soo Soh

Keyword(s):

Arabidopsis Thaliana ◽

Red Light ◽

Light Responses

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Ultra-High-Density QTL Marker Mapping for Seedling Photomorphogenesis Mediating Arabidopsis Establishment in Southern Patagonia

Frontiers in Plant Science ◽

10.3389/fpls.2021.677728 ◽

2021 ◽

Vol 12 ◽

Author(s):

Daniel Matsusaka ◽

Daniele Filiault ◽

Diego H. Sanchez ◽

Javier F. Botto

Keyword(s):

Complex Traits ◽

Red Light ◽

High Density ◽

Potential Candidate ◽

Hypocotyl Length ◽

Light Responses ◽

Wide Range ◽

Southern Patagonia ◽

Ril Population ◽

Wild Accessions

Arabidopsis thaliana shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, Arabidopsis has a high potential for the identification of genes underlying ecologically important complex traits, thus providing new insights on genome evolution. Previous research suggested that distinct light responses were crucial for Arabidopsis establishment in a peculiar ecological niche of southern Patagonia. The aim of this study was to explore the genetic basis of contrasting light-associated physiological traits that may have mediated the rapid adaptation to this new environment. From a biparental cross between the photomorphogenic contrasting accessions Patagonia (Pat) and Columbia (Col-0), we generated a novel recombinant inbred line (RIL) population, which was entirely next-generation sequenced to achieve ultra-high-density saturating molecular markers resulting in supreme mapping sensitivity. We validated the quality of the RIL population by quantitative trait loci (QTL) mapping for seedling de-etiolation, finding seven QTLs for hypocotyl length in the dark and continuous blue light (Bc), continuous red light (Rc), and continuous far-red light (FRc). The most relevant QTLs, Rc1 and Bc1, were mapped close together to chromosome V; the former for Rc and Rc/dark, and the latter for Bc, FRc, and dark treatments. The additive effects of both QTLs were confirmed by independent heterogeneous inbred families (HIFs), and we explored TZP and ABA1 as potential candidate genes for Rc1 and Bc1QTLs, respectively. We conclude that the Pat × Col-0 RIL population is a valuable novel genetic resource to explore other adaptive traits in Arabidopsis.

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