FIN5 Positively Regulates Far-red Light Responses in Arabidopsis thaliana

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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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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Loss of the ETR1 ethylene receptor reduces the inhibitory effect of far-red light and darkness on seed germination of Arabidopsis thaliana

Frontiers in Plant Science ◽

10.3389/fpls.2014.00433 ◽

2014 ◽

Vol 5 ◽

Cited By ~ 13

Author(s):

Rebecca L. Wilson ◽

Arkadipta Bakshi ◽

Brad M. Binder

Keyword(s):

Arabidopsis Thaliana ◽

Seed Germination ◽

Red Light ◽

Inhibitory Effect ◽

Ethylene Receptor

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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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A Multifaceted Action of Phytochrome B in Plant Environmental Adaptation

Frontiers in Plant Science ◽

10.3389/fpls.2021.659712 ◽

2021 ◽

Vol 12 ◽

Author(s):

Jae Young Kim ◽

June-Hee Lee ◽

Chung-Mo Park

Keyword(s):

Red Light ◽

Environmental Adaptation ◽

Signaling Cascades ◽

Adaptive Behaviors ◽

Environmental Cues ◽

Plant Responses ◽

Light Illumination ◽

Light Responses ◽

And Performance

Light acts as a vital external cue that conveys surrounding information into plant growth and performance to facilitate plants to coordinate with changing environmental conditions. Upon exposure to light illumination, plants trigger a burst of molecular and physiological signaling cascades that induces not only photomorphogenic responses but also diverse adaptive behaviors. Notably, light responses and photomorphogenic traits are often associated with plant responses to other environmental cues, such as heat, cold, drought, and herbivore and pathogen attack. Growing evidence in recent years demonstrate that the red/far-red light-absorbing phytochrome (phy) photoreceptors, in particular phyB, play an essential role in plant adaptation responses to abiotic and biotic tensions by serving as a key mediator of information flow. It is also remarkable that phyB mediates the plant priming responses to numerous environmental challenges. In this minireview, we highlight recent advances on the multifaceted role of phyB during plant environmental adaptation. We also discuss the biological relevance and efficiency of the phy-mediated adaptive behaviors in potentially reducing fitness costs under unfavorable environments.

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