Improving the Predictive Value of Phytochrome Photoequilibrium: Consideration of Spectral Distortion Within a Leaf

Abstract

The ratio of active phytochrome (Pfr) to total phytochrome (Pr + Pfr), called phytochrome photo-equilibrium (PPE; also called phytochrome photostationary state, PSS) has been used to explain shade avoidance responses in both natural and controlled environments. PPE is commonly estimated using measurements of the spectral photon distribution (SPD) above the canopy and photoconversion coefficients. This approach has effectively predicted morphological responses when only red and far-red (FR) photon fluxes have varied, but controlled environment research often utilizes unique ratios of wavelengths so a more rigorous evaluation of the predictive ability of PPE on morphology is warranted. Estimations of PPE have rarely incorporated the optical effects of spectral distortion within a leaf caused by pigment absorbance and photon scattering. We studied stem elongation rate in the model plant cucumber under diverse spectral backgrounds over a range of one to 45% FR (total photon flux density, 400–750 nm, of 400 μmol m–2 s–1) and found that PPE was not predictive when blue and green varied. Preferential absorption of red and blue photons by chlorophyll results in an SPD that is relatively enriched in green and FR at the phytochrome molecule within a cell. This can be described by spectral distortion functions for specific layers of a leaf. Multiplying the photoconversion coefficients by these distortion functions yields photoconversion weighting factors that predict phytochrome conversion at the site of photon perception within leaf tissue. Incorporating spectral distortion improved the predictive value of PPE when phytochrome was assumed to be homogeneously distributed within the whole leaf. In a supporting study, the herbicide norflurazon was used to remove chlorophyll in seedlings. Using distortion functions unique to either green or white cotyledons, we came to the same conclusions as with whole plants in the longer-term study. Leaves of most species have similar spectral absorbance so this approach for predicting PPE should be broadly applicable. We provide a table of the photoconversion weighting factors. Our analysis indicates that the simple, intuitive ratio of FR (700–750 nm) to total photon flux (far-red fraction) is also a reliable predictor of morphological responses like stem length.

Retrograde and anterograde signaling in the crosstalk between chloroplast and nucleus

“…Massive transcriptional reprogramming of both the nuclear and plastid genomes, as well as the onset of a complex signaling interconnecting network, accompany these morphological changes in response to light. This process is called photomorphogenesis and it includes numerous and poorly understood light-sensing mechanisms (Kusuma and Bugbee, 2021).…”

“…According to their absorption spectrum, these photoreceptors may be divided into different groups: one UV-B light receptor (UVR8) in Arabidopsis, three cryptochromes (CRY1-CRY3), two phototropins (PHOT1 and PHOT2), and three Zeitlupe family (ZTL) proteins detecting UV-A/blue light, and five phytochromes (PHYA-PHYE) absorbing red (R)/far-red (FR) light (Kleine et al, 2003;Chory, 2010). These light receptors interact in synergistic, antagonistic, and redundant ways with each other (Mazzella, 2001;Pfannschmidt and Liere, 2005;Pfannschmidt, 2010;Kusuma and Bugbee, 2021).…”

“…Photobodies are sites for protein degradation and/or transcription factors, as they colocalize with a variety of transcriptional regulators and their E3 ubiquitin ligases as well as photoreceptors (Possingham, 1980;Pogson et al, 2015). Photobodies change in size and quantity in response to changes in light, developmental phases, and daily rhythms (Possingham, 1980;Pesaresi et al, 2007;Van Buskirk et al, 2014;Kusuma and Bugbee, 2021).…”

Layering contrasting photoselective filters improves the simulation of foliar shade

“…Plants have been shown to respond to reductions in the ratio of the quantity of P fr to the total amount of phytochrome, termed the phytochrome photoequilibrium (PPE; P fr /total phytochrome, or the phytochrome photostationary state) [ 11 ]. The PPE can be estimated using spectrophotometric data [ 13 ], but is influenced by weighting factors that take into account items such as phytochrome extinction coefficients and quantum yields of photoconversion [ 14 , 15 ]. Weighting factors from various authors differ due to the source and quality of purified phytochrome used to develop said weighting factors [ 16 ], but the most commonly used factors from Kelly and Lagarias [ 17 ] and Sager et al [ 13 ] lead to similar results when on a normalized scale [ 15 ].…”

Diatom phytochromes integrate the entire visible light spectra for photosensing in marine environments

“…Globally, the sensitivity matches with Pr and Pfr absorption spectra with peaks in B, R and FR lights (Fig.2C), but, surprisingly, FR light appears less efficient compared to other wavelengths. This decreased FR sensitivity could be due to different events, e.g., light distortion inside the cell (14, 15) , an energetic barrier for low energy FR photons, or signaling events following DPH light absorption in FR compared to other wavebands (16) . This is also observed with dph reporter lines complemented with the Thalassiosira pseudonana DPH, which is more closely related to the DPH found in the open ocean from centric species (Fig.S5, DataS1).…”