Phosphorylation of Phytochrome B Inhibits Light-Induced Signaling via Accelerated Dark Reversion in <i>Arabidopsis</i>

Medzihradszky, Mátyás; Bindics, János; Ádám, Éva; Viczián, András; Klement, Éva; Lorrain, Séverine; Gyula, Péter; Mérai, Zsuzsanna; Fankhauser, Christian; Medzihradszky, Katalin F.; Kunkel, Tim; Schäfer, Eberhard; Nagy, Ferenc

doi:10.1105/tpc.112.106898

Cited by 112 publications

(149 citation statements)

References 51 publications

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“…Furthermore, each phytochrome shows strong dark reversion in some species (29). PhyB, exhibiting a fast and strong but incomplete dark conversion in some cases, is the main light receptor responsible for the shade-avoidance response in mature plants (30) and shows evidence of positive selection in A. duranensis (Fig. 3B), suggesting a role in skotomorphogenesis.…”

Section: Resultsmentioning

confidence: 99%

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

Chen

Li²,

Pandey

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

214

222

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Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45-56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis. For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.

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Section: Resultsmentioning

confidence: 99%

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

Chen

Li²,

Pandey

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

214

222

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“…Unlike most bacterial Phys, plant Phys contain a long glycine/serine-rich NTE that is critical to the normal absorption of the photoreceptor and stability of Pfr (1, 4) as well as biological activity, possibly through its light-dependent phosphorylation (27,28). For example, NTE deletion mutants, such as PhyB(90-624), display hypsochromically shifted absorption maxima and more rapid thermal reversion (Fig.…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome

Burgie

Bussell

Walker

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

201

327

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Many aspects of plant photomorphogenesis are controlled by the phytochrome (Phy) family of bilin-containing photoreceptors that detect red and far-red light by photointerconversion between a dark-adapted Pr state and a photoactivated Pfr state. Whereas 3D models of prokaryotic Phys are available, models of their plant counterparts have remained elusive. Here, we present the crystal structure of the photosensing module (PSM) from a seed plant Phy in the Pr state using the PhyB isoform from Arabidopsis thaliana. The PhyB PSM crystallized as a head-to-head dimer with strong structural homology to its bacterial relatives, including a 5(Z)syn, 10(Z)syn, 15(Z)anti configuration of the phytochromobilin chromophore buried within the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) domain, and a well-ordered hairpin protruding from the Phy-specific domain toward the bilin pocket. However, its Per/Arnt/Sim (PAS) domain, knot region, and helical spine show distinct structural differences potentially important to signaling. Included is an elongated helical spine, an extended β-sheet connecting the GAF domain and hairpin stem, and unique interactions between the region upstream of the PAS domain knot and the bilin A and B pyrrole rings. Comparisons of this structure with those from bacterial Phys combined with mutagenic studies support a toggle model for photoconversion that engages multiple features within the PSM to stabilize the Pr and Pfr end states after rotation of the D pyrrole ring. Taken together, this Arabidopsis PhyB structure should enable molecular insights into plant Phy signaling and provide an essential scaffold to redesign their activities for agricultural benefit and as optogenetic reagents.G iven the importance of sunlight to their survival and growth, plants have adopted a collection of photoreceptors and interconnected signaling cascades to optimize their photosynthetic potential and synchronize their lifecycles with circadian and seasonal rhythms. Chief among these are the phytochromes (Phys), a family of bilin (or open-chain tetrapyrrole)-containing red/far-red light-absorbing photoreceptors that provides spatial and time-dependent information by sensing the fluence rate, direction, duration, and color of a plant's light environment (1, 2). This information then regulates nearly all aspects of plant growth and development from seed germination to senescence. Notably, seed plants typically express three Phy isoforms (PhyA, PhyB, and PhyC) that control distinct and overlapping photoresponses, with PhyB having a dominant role in green tissues (2, 3).Phys are homodimers with each sister polypeptide divided into an N-terminal photosensory module (PSM) that absorbs light followed by an output module (OPM) that promotes dimerization and presumably, relays the light signals (1, 4). The PSM sequentially contains a Per/Arnt/Sim (PAS) domain of unknown function, a cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) domain that cradles the bilin, and a Phy-specific (PHY) domain that stabilizes the photoactivated ...

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“…Unlike bacterial Phys, plant Phys include a long glycine/serinerich NTE beyond the PAS domain that is especially important for the thermal stability of the Pfr state (Burgie et al, 2014a) and proper biological activity, possibly via its light-dependent phosphorylation (Cherry et al, 1992;Medzihradszky et al, 2013;Nito et al, 2013). The 3D model of At-PhyB containing much of the NTE revealed an unexpected contact between this extension and PFB that helps explain some of these effects.…”

Section: Structural Resolution Of a Plant Phymentioning

confidence: 99%

Phytochromes: An Atomic Perspective on Photoactivation and Signaling

2014

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Phosphorylation of Phytochrome B Inhibits Light-Induced Signaling via Accelerated Dark Reversion in Arabidopsis

Cited by 112 publications

References 51 publications

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens

Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome

Phytochromes: An Atomic Perspective on Photoactivation and Signaling

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