Preferred Basis in a Measurement Process

The effect of decoherence is analysed for a free particle, interacting with an environment via a dissipative coupling. The interaction between the particle and the environment occurs by a coupling of the position operator of the particle with the environmental degrees of freedom. By examining the exact solution of the density matrix equation one finds that the density matrix becomes completely diagonal in momentum with time while the position space density matrix remains nonlocal. This establishes the momentum basis as the emergent 'preferred basis' selected by the environment which is contrary to the general expectation that position should emerge as the preferred basis since the coupling with the environment is via the position coordinate.Comment: Standard REVTeX format, 10 pages of output. Accepted for publication in Phys. Rev

Residues Clustered in the Light-Sensing Knot of Phytochrome B are Necessary for Conformer-Specific Binding to Signaling Partner PIF3

The bHLH transcription factor, PHYTOCHROME INTERACTING FACTOR 3 (PIF3), interacts specifically with the photoactivated, Pfr, form of Arabidopsis phytochrome B (phyB). This interaction induces PIF3 phosphorylation and degradation in vivo and modulates phyB-mediated seedling deetiolation in response to red light. To identify missense mutations in the phyB N-terminal domain that disrupt this interaction, we developed a yeast reverse-hybrid screen. Fifteen individual mutations identified in this screen, or in previous genetic screens for Arabidopsis mutants showing reduced sensitivity to red light, were shown to also disrupt light-induced binding of phyB to PIF3 in in vitro co-immunoprecipitation assays. These phyB missense mutants fall into two general classes: Class I (eleven mutants) containing those defective in light signal perception, due to aberrant chromophore attachment or photoconversion, and Class II (four mutants) containing those normal in signal perception, but defective in the capacity to transduce this signal to PIF3. By generating a homology model for the three-dimensional structure of the Arabidopsis phyB chromophore-binding region, based on the crystal structure of Deinococcus radiodurans phytochrome, we predict that three of the four Class II mutated phyB residues are solvent exposed in a cleft between the presumptive PAS and GAF domains. This deduction suggests that these residues could be directly required for the physical interaction of phyB with PIF3. Because these three residues are also necessary for phyB-imposed inhibition of hypocotyl elongation in response to red light, they are functionally necessary for signal transfer from photoactivated phyB, not only to PIF3 and other related bHLH transcription factors tested here, but also to other downstream signaling components involved in regulating seedling deetiolation

FHY1 Mediates Nuclear Import of the Light-Activated Phytochrome A Photoreceptor

The phytochrome (phy) family of photoreceptors is of crucial importance throughout the life cycle of higher plants. Light-induced nuclear import is required for most phytochrome responses. Nuclear accumulation of phyA is dependent on two related proteins called FHY1 (Far-red elongated HYpocotyl 1) and FHL (FHY1 Like), with FHY1 playing the predominant function. The transcription of FHY1 and FHL are controlled by FHY3 (Far-red elongated HYpocotyl 3) and FAR1 (FAr-red impaired Response 1), a related pair of transcription factors, which thus indirectly control phyA nuclear accumulation. FHY1 and FHL preferentially interact with the light-activated form of phyA, but the mechanism by which they enable photoreceptor accumulation in the nucleus remains unsolved. Sequence comparison of numerous FHY1-related proteins indicates that only the NLS located at the N-terminus and the phyA-interaction domain located at the C-terminus are conserved. We demonstrate that these two parts of FHY1 are sufficient for FHY1 function. phyA nuclear accumulation is inhibited in the presence of high levels of FHY1 variants unable to enter the nucleus. Furthermore, nuclear accumulation of phyA becomes light- and FHY1-independent when an NLS sequence is fused to phyA, strongly suggesting that FHY1 mediates nuclear import of light-activated phyA. In accordance with this idea, FHY1 and FHY3 become functionally dispensable in seedlings expressing a constitutively nuclear version of phyA. Our data suggest that the mechanism uncovered in Arabidopsis is conserved in higher plants. Moreover, this mechanism allows us to propose a model explaining why phyA needs a specific nuclear import pathway

Phytochrome A function in red light sensing

Light signals perceived by the phytochrome family of red (R) and far-red (FR) light-absorbing photoreceptors direct plant growth and development throughout their lifecycle. In contrast to other family members, phyA displays rapid light-induced proteolytic degradation upon conversion to the biologically active Pfr form and mediates high irradiance responses to continuous FR. These unique properties together with limited examples of phyA function in R have resulted in an over-simplified portrayal of phyA as a FR sensor which acts predominantly in seed germination and early stages of seedling de-etiolation. In a recent work, published in The Plant Journal, we report significant phyA activity in Arabidopsis thaliana at high (>100 µmolm(−2)s(−1)) photon irradiances of R. Under these conditions, we observed retarded degradation of a pool of nuclear-localised phyA, consistent with the phenomenon of photoprotection, and showed phyBphyCphyDphyE quadruple null mutants, containing only functional phyA, to de-etiolate and survive to flowering. The photon irradiances used in this study were greater than those routinely used for photomorphogenic analysis in the laboratory but considerably lower than those commonly observed in daylight. In this addendum we present additional analyses of the phyBphyCphyDphyE mutant and discuss the possibility that phyA may perform a significant role in the growth and development of daylight-grown plants

Phytochromes and shade avoidance responses in plants

• Background and Aims The ability to detect and respond to the impending threat of shade can confer significant selective advantage to plants growing in natural communities. This Botanical Briefing highlights (a) the regulation of shade-avoidance responses by endogenous and exogenous factors and (b) current understanding of the molecular components involved in red to far-red ratio signal transduction. • Scope The Briefing covers: (a) the shade-avoidance syndrome in higher plants; (b) the adaptive significance of shade avoidance in natural light environments; (c) phytochrome regulation of shade-avoidance responses; (d) the role of blue light signals in shade avoidance; (e) gating of rapid shade-avoidance responses by the circadian clock; (f) potential signalling components and future perspectives