Phytochromes are a widespread family of red/far-red responsive photoreceptors first discovered in plants, where they constitute one of the three main classes of photomorphogenesis regulators. All phytochromes utilize covalently attached bilin chromophores that enable photoconversion between red-absorbing (Pr) and far-red-absorbing (Pfr) forms. Phytochromes are thus photoswitchable photosensors; canonical phytochromes have a conserved N-terminal photosensory core and a C-terminal regulatory region, which typically includes a histidine-kinase-related domain. The discovery of new bacterial and cyanobacterial members of the phytochrome family within the last decade has greatly aided biochemical and structural characterization of this family, with the first crystal structure of a bacteriophytochrome photosensory core appearing in 2005. This structure and other recent biochemical studies have provided exciting new insights into the structure of phytochrome, the photoconversion process that is central to...

/pdf/phytochrome-structure-and-signaling-mechanisms-bwi9ybrw78.pdf

Phytochrome structure and signaling mechanisms

Light is life for plants. To continuously assess and adapt to fluctuations in the quality and quantity of this essential commodity, plants deploy sensory photoreceptors, including the phytochromes. Having captured an incoming photon, the activated phytochrome molecule must relay this information to nuclear genes that are poised to respond by directing appropriate adjustments in growth and development. Defining the intricate intracellular signalling networks through which this sensory information is transduced is an area of intense research activity.

Phytochrome photosensory signalling networks

A phylogenetic analysis of more than 350 multicopper oxidases (MCOs) from fungi, insects, plants, and bacteria provided the basis for a refined classification of this enzyme family into laccases sensu stricto (basidiomycetous and ascomycetous), insect laccases, fungal pigment MCOs, fungal ferroxidases, ascorbate oxidases, plant laccase-like MCOs, and bilirubin oxidases. Within the largest group of enzymes, formed by the 125 basidiomycetous laccases, the gene phylogeny does not strictly follow the species phylogeny. The enzymes seem to group at least partially according to the lifestyle of the corresponding species. Analyses of the completely sequenced fungal genomes showed that the composition of MCOs in the different species can be very variable. Some species seem to encode only ferroxidases, whereas others have proteins which are distributed over up to four different functional clusters in the phylogenetic tree.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1742-4658.2006.05247.x

Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences

Predictions of temperature rise over the twenty-first century are necessarily uncertain, both because the sensitivity of the climate system to changing atmospheric greenhouse-gas concentrations, as well as the rate of ocean heat uptake, is poorly quantified and because future influences on climate-of anthropogenic as well as natural origin-are difficult to predict. Past observations have been used to help constrain the range of uncertainties in future warming rates, but under the assumption of a particular scenario of future emissions. Here we investigate the relative importance of the uncertainty in climate response to a particular emissions scenario versus the uncertainty caused by the differences between future emissions scenarios for our estimates of future change. We present probabilistic forecasts of global-mean temperatures for four representative scenarios for future emissions, obtained with a comprehensive climate model. We find that, in the absence of policies to mitigate climate change, global-mean temperature rise is insensitive to the differences in the emissions scenarios over the next four decades. We also show that in the future, as the signal of climate change emerges further, the predictions will become better constrained.

/pdf/origins-and-estimates-of-uncertainty-in-predictions-of-e0pme4x340.pdf

Origins and estimates of uncertainty in predictions of twenty-first century temperature rise

Sensory proteins must relay structural signals from the sensory site over large distances to regulatory output domains. Phytochromes are a major family of red-light-sensing kinases that control diverse cellular functions in plants, bacteria and fungi. Bacterial phytochromes consist of a photosensory core and a carboxy-terminal regulatory domain. Structures of photosensory cores are reported in the resting state and conformational responses to light activation have been proposed in the vicinity of the chromophore. However, the structure of the signalling state and the mechanism of downstream signal relay through the photosensory core remain elusive. Here we report crystal and solution structures of the resting and activated states of the photosensory core of the bacteriophytochrome from Deinococcus radiodurans. The structures show an open and closed form of the dimeric protein for the activated and resting states, respectively. This nanometre-scale rearrangement is controlled by refolding of an evolutionarily conserved 'tongue', which is in contact with the chromophore. The findings reveal an unusual mechanism in which atomic-scale conformational changes around the chromophore are first amplified into an angstrom-scale distance change in the tongue, and further grow into a nanometre-scale conformational signal. The structural mechanism is a blueprint for understanding how phytochromes connect to the cellular signalling network.

/pdf/signal-amplification-and-transduction-in-phytochrome-436ofoe9j0.pdf

Signal amplification and transduction in phytochrome photosensors

Phytochromes comprise a principal family of red/far-red light sensors in plants. Although phytochromes were thought originally to be confined to photosynthetic organisms, we have recently detected phytochrome-like proteins in two heterotrophic eubacteria, Deinococcus radiodurans and Pseudomonas aeruginosa. Here we show that these form part of a widespread family of bacteriophytochromes (BphPs) with homology to two-component sensor histidine kinases. Whereas plant phytochromes use phytochromobilin as the chromophore, BphPs assemble with biliverdin, an immediate breakdown product of haem, to generate photochromic kinases that are modulated by red and far-red light. In some cases, a unique haem oxygenase responsible for the synthesis of biliverdin is part of the BphP operon. Co-expression of this oxygenase with a BphP apoprotein and a haem source is sufficient to assemble holo-BphP in vivo. Both their presence in many diverse bacteria and their simplified assembly with biliverdin suggest that BphPs are the progenitors of phytochrome-type photoreceptors.

Bacteriophytochromes are photochromic histidine kinases using a biliverdin chromophore

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Bacteriophytochromes are photochromic histidine kinases using a biliverdin chromophore