Hyperactivity of the Arabidopsis cryptochrome (cry1) L407F mutant is caused by a structural alteration close to the cry1 ATP-binding site

Bridging the Gap: From Photoperception to the Transcription Control of Genes Related to the Production of Phenolic Compounds

Phenolic compounds are a group of secondary metabolites responsible for several processes in plants-these compounds are involved in plant-environment interactions (attraction of pollinators, repelling of herbivores, or chemotaxis of microbiota in soil), but also have antioxidative properties and are capable of binding heavy metals or screening ultraviolet radiation. Therefore, the accumulation of these compounds has to be precisely driven, which is ensured on several levels, but the most important aspect seems to be the control of the gene expression. Such transcriptional control requires the presence and activity of transcription factors (TFs) that are driven based on the current requirements of the plant. Two environmental factors mainly affect the accumulation of phenolic compounds-light and temperature. Because it is known that light perception occurs via the specialized sensors (photoreceptors) we decided to combine the biophysical knowledge about light perception in plants with the molecular biology-based knowledge about the transcription control of specific genes to bridge the gap between them. Our review offers insights into the regulation of genes related to phenolic compound production, strengthens understanding of plant responses to environmental cues, and opens avenues for manipulation of the total content and profile of phenolic compounds with potential applications in horticulture and food production.

The blue light signaling inhibitor 3-bromo-7-nitroindazole affects gene translation at the initial reception of blue light in young Arabidopsis seedlings

Initial light reception after germination is a dramatic life event when a seedling starts proper morphogenesis. Blue light contains a range of light wavelengths that plants can perceive. A previous report suggested that the chemical compound 3-bromo-7-nitroindazole (3B7N) inhibits blue light-mediated suppression of hypocotyl elongation by physically interacting with the blue light receptor Cryptochrome 1 (CRY1). We previously examined changes of genome-wide gene expression in Arabidopsis seedlings germinated in the dark and then exposed to blue light by RNA-seq and Ribo-seq analyses. The expression of ribosome-related genes was translationally upregulated in response to the initial blue light exposure, depending on signals from both the nucleus and chloroplasts. Here, we re-analyzed our previous data and examined the effect of 3B7N treatment on changes in gene expression upon blue light exposure. The results showed that 3B7N negatively affected translation of ribosome-related genes and, interestingly, the effects were similar to not only those in cry1cry2 mutants but also plants under suppression of photosynthesis. We propose an apparent crosstalk between chloroplast function and blue light signaling.

ATP binding promotes light-induced structural changes to the protein moiety of Arabidopsis cryptochrome 1

Cryptochromes (CRYs) are blue-light receptors involved in photomorphogenesis in plants. Flavin adenine dinucleotide (FAD) is one of the chromophores of cryptochromes; its resting state oxidized form is converted into a signalling state neutral semiquionod radical (FADH˙) form. Studies have shown that cryptochrome 1 from Arabidopsis thaliana (AtCRY1) can bind ATP at its photolyase homology region (PHR), resulting in accumulation of FADH˙ form. This study used light-induced difference Fourier transform infrared spectroscopy to investigate how ATP influences structural changes in AtCRY1-PHR during the photoreaction. In the presence of ATP, there were large changes in the signals from the protein backbone compared with in the absence of ATP. The deprotonation of a carboxylic acid was observed only in the presence of ATP; this was assigned as aspartic acid (Asp) 396 through measurement of Asp to glutamic acid mutants. This corresponds to the protonation state of Asp396 estimated from the reported pKa values of Asp396; that is, the side chain of Asp396 is deprotonated and protonated for the ATP-free and -bound forms, respectively, in our experimental condition at pH8. Therefore, Asp396 acts a proton donor to FAD when it is ptotonated. It was indicated that the protonation/deprotination process of Asp396 is correlated with the accunumulation of FADH˙ and protein conformational changes.

Method for Phenotypic Chemical Screening to Identify Cryptochrome Inhibitors

After germination, plants determine their morphogenesis, such as hypocotyl elongation and cotyledon opening, by responding to various wavelengths of light (photomorphogenesis). Cryptochrome is a blue-light photoreceptor that controls de-etiolation, stomatal opening and closing, flowering time, and shade avoidance. Successful incorporation of these phenotypes as indicators into a chemical screening system results in faster selection of candidate compounds. Here, we describe phenotypic screening for the blue-light response of Arabidopsis thaliana seedling and the resulting process that clarifies that the compound obtained in the screening is an inhibitor of cryptochromes.

The Arabidopsis cryptochrome 2 I404F mutant is hypersensitive and shows flavin reduction even in the absence of light

The cryptochrome photoreceptor mutant cry2I404F exhibits hyperactivity in the dark, hypersensitivity in different light conditions, and in contrast to the wild-type protein, its flavin chromophore is reducible even in the absence of light. Plant cryptochromes (cry) are blue-light photoreceptors involved in multiple signaling pathways and various photomorphogenic responses. One biologically hyperactive mutant of a plant cryptochrome that was previously characterized is Arabidopsis cry1L407F (Exner et al. in Plant Physiol 154:1633-1645, 2010). Protein sequence alignments of different cryptochromes revealed that L407 in cry1 corresponds to I404 in cry2. Point mutation of Ile to Phe in cry2 in this position created a novel mutant. The present study provided a baseline data on the elucidation of the properties of cry2I404F. This mutant was still able to bind ATP-triggering conformational changes, as confirmed by partial tryptic digestion and thermo-FAD assays. Surprisingly, the FAD cofactor of cry2I404F was reduced by the addition of reductant even in the absence of light. In vivo, cry2I404F exhibited a cop phenotype in the dark and hypersensitivity to various light conditions compared to cry2 wild type. Overall, these data suggest that the hypersensitivity to red and blue light and hyperactivity of this novel mutant in the dark can be mostly accounted to structural alterations brought forth by the Ile to Phe mutation at position 404 that allows reduction of the flavin chromophore even in the absence of light.

ATP boosts lit state formation and activity of Arabidopsis cryptochrome 2

Cryptochrome (cry) blue light photoreceptors have important roles in the regulation of plant development. Their photocycle includes redox changes of their flavin adenine dinucleotide (FAD) chromophore, which is fully oxidised in the dark state and semi-reduced in the signalling-active lit state. The two Arabidopsis thaliana cryptochromes, cry1 and cry2, and the plant-type cryptochrome CPH1 from Chlamydomonas rheinhardtii bind ATP and other nucleotides. Binding of ATP affects the photocycle of these photoreceptors and causes structural alterations. However, the exact regions that undergo structural changes have not been defined, and most importantly it is not known whether ATP binding affects the biological activity of these photoreceptors in planta. Here we present studies on the effect of ATP on Arabidopsis cry2. Recombinant cry2 protein showed a high affinity for ATP (K_D of 1.09 ± 0.48 μm). Binding of ATP and other adenines promoted photoreduction of the FAD chromophore in vitro and caused structural changes, particularly in α-helix 21 which links the photosensory domain with the C-terminal extension. The constructed cry2Y399A mutant was unable to bind ATP and did not show enhancement of photoreduction by ATP. When this mutant gene was expressed in Arabidopsis null cry2 mutant plants it retained some biological activity, which was, however, lower than that of the wild type. Our results indicate that binding of ATP to cry2, and most likely to other plant-type cryptochromes, is not essential but boosts the formation of the signalling state and biological activity.