InterPro/domain-derived annotations capture phytochrome family features, but phosphorelay-specific inferences should be interpreted cautiously for plant PHYA because the family context supports photoreceptor signaling.

The IBA phosphorelay sensor kinase call follows a broad phylogenetic inference across histidine-kinase-like photoreceptors and is not specific enough for Arabidopsis PHYA's experimentally supported output.

UniProt subcellular-location mappings for cytoplasm, nucleoplasm, and nuclear speck are consistent with PHYA's light-dependent cytoplasmic to nuclear redistribution.

Logical inference from far-red photoreceptor activity is appropriate for far-red signaling pathway, but not for phosphorelay signal transduction system when the underlying kinase call is rejected.

ARBA's identical protein binding annotation is consistent with phytochrome dimerization but should be represented by the more informative homodimerization term.

AtSubP computational predictions to plasma membrane and chloroplast are not supported by the curated PHYA literature or UniProt localization.

UniProt summarizes PHYA as a regulatory red/far-red photoreceptor that shuttles between cytoplasm and nucleus and contains covalently linked phytochromobilin.

The deep research synthesis supports PHYA as a conserved red/far-red photoreceptor specialized for very-low-fluence and far-red high-irradiance responses.

PANTHER PTHR47876 defines the family as plant phytochrome photoreceptors, matching PHYA's experimentally supported core role.

PHYA (P14712) is listed in PTHR47876:SF3 together with plant phytochrome A/B/C/D/E family members.

PKS1 is a phytochrome-binding substrate for light-regulated phytochrome kinase activity, supporting PHYA pathway interactions and kinase output without making generic protein binding a useful core MF.

NDPK2 preferentially binds activated phytochrome in vitro and acts as a positive phytochrome signaling component.

HFR1 is a phyA signaling component, but the paper reports that HFR1 did not directly bind phyA or phyB in the tested assay.

phyA binds PIF3 selectively and reversibly after photoconversion to Pfr, but with lower apparent affinity than phyB.

PIF4 is primarily a phyB pathway factor and has little affinity for phyA, arguing against a strong PHYA-specific protein-binding annotation.

PHYA-GFP translocates from cytosol to nucleus under continuous far-red light and nuclear spots are linked to HIR signaling.

phyA and phyB mediate red-light-based root phototropism, whereas root gravitropism defects in this abstract are attributed to phyB and phyAB, not phyA alone.

Light promotes phyA/phyB interaction with PIF3 and phytochrome-dependent PIF3 degradation during the dark-to-light transition.

All five Arabidopsis phytochromes are present as dimers, while type II phytochromes can form heterodimers.

PIF1 interacts with photoactivated phytochromes A and B and links phytochrome signaling to chlorophyll biosynthesis regulation.

The abstract supports roles for phytochromes in root elongation and gravitropic curvature, but does not establish a PHYA single-mutant gravitropism defect.

PAPP5 dephosphorylates active phytochromes and tunes phytochrome stability and affinity for NDPK2.

FHY1 physically interacts with PHYA and is required for light-regulated PHYA nuclear accumulation.

FHY1 and FHL jointly mediate PHYA nuclear accumulation and colocalize with PHYA in nuclear speckles.

PHYA has a quantitatively dominant early role in red-light-induced gene expression during seedling de-etiolation.

phyA loss-of-function alleles show increased arsenic tolerance, indicating non-core stress-response crosstalk.

PHYA phosphorylation state controls differential association with FHY1/FHY3 signaling intermediates and COP1/SPA attenuation machinery.

PHYA directly interacts with FHY1/FHL and recombinant PHYA phosphorylates FHY1 in vitro.

PHYA is present as a homodimer and interacts with PIF3 in vivo after red light in an FR-reversible manner.

PHYA, FHY1, FHL, LAF1, and HFR1 form protein complexes that transmit far-red PHYA signals for de-etiolation.

The response peak of PHYA in far-red light is determined by photoconversion and FHY1/FHL nuclear-import complex dynamics.

A PHYA N-terminal mutant has reduced FHY1/FHL binding, impaired nuclear import, and reduced VLFR/HIR signaling.

The Pfr form of phytochromes can regulate PORA mRNA translation in the cytosol through PNT1; PHYA involvement is suggested but not resolved as a core PHYA function.

Photoactivated phytochromes directly interact with HEMERA to promote HMR accumulation, photobody localization, and PIF degradation.

This review summarizes phytochrome-PIF regulation and stimulus-responsive PIF expression, but the cached text does not validate a PHYA-specific cold response annotation.

The high-throughput mRNA interactome study captured more than 700 Arabidopsis proteins, but the cached text does not provide PHYA-specific mechanistic mRNA-binding evidence.

PIF8 represses PHYA-mediated far-red responses mainly through indirect pathway effects and binds PHYA weakly, if at all.

The cached abstract describes a light and water-withdrawal screen but does not provide PHYA-specific evidence for a generic light-response annotation.

HY8 is PHYA; hy8 mutants lacking functional PHYA are defective in prolonged far-red high-irradiance responses.

PHYA initiates very-low-fluence and far-red high-irradiance response pathways in Arabidopsis seedlings.

PIF3 binds phyA/phyB C-terminal domains and acts in phytochrome signaling to photoregulated genes.