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The Synechocystis sp. PCC6803 can move on a solid surface in response to light, a phenomenon called phototaxis. Although many of the photoreceptors involved in phototaxis have been identified, the mechanisms that regulate directional motility of Synechocystis are not well understood. Previous studies showed that a mutant lacking the blue light-using flavin (BLUF) photoreceptor PixD exhibits negative phototaxis under conditions where the wild type responds positively. PixD interacts with the pseudo-response regulator-like protein PixE in a light-dependent manner, suggesting that this intermolecular interaction is important for phototaxis regulation, although genetic evidence has been lacking. To gain further insight into phototaxis regulation by PixD-PixE signaling, we constructed the deletion mutants ΔPixE and ΔPixD-ΔPixE, and characterized their phenotypes, which matched those of the wild type (positive phototaxis). Because ΔPixD exhibited negative phototaxis, PixE must function downstream of PixD. Under intense blue light (>100 μmol m-2 s-1; 470 nm) the wild type exhibited negative phototaxis, but ΔPixD-PixE exhibited positive phototaxis toward low-intensity blue light (∼0.8 μmol m-2 s-1; 470 nm). These results suggest that an unknown light-sensing system(s), that is necessary for directional cell movement, can be activated by low-intensity blue light; on the other hand, PixD needs high-intensity blue light to be activated. We also isolated spontaneous mutants that compensated for the pixE deletion. Genome-wide sequencing of the mutants revealed that the uncharacterized gene sll2003 regulates positive and negative phototaxis in response to light intensity., (© The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Plants have a remarkable ability to perceive and respond to various wavelengths of light and initiate regulation of different cascades of light signaling and molecular components. While the perception of red light and the mechanisms of its signaling involving phytochromes are largely known, knowledge of the mechanisms of blue light signaling is still limited. Chemical genetics involves the use of diverse small active or synthetic molecules to evaluate biological processes. By combining chemicals and analyzing the effects they have on plant morphology, we identified a chemical, 3-bromo-7-nitroindazole (3B7N), that promotes hypocotyl elongation of wild-type Arabidopsis only under continuous blue light. Further evaluation with loss-of-function mutants confirmed that 3B7N inhibits photomorphogenesis through cryptochrome-mediated light signaling. Microarray analysis demonstrated that the effect of 3B7N treatment on gene expression in cry1cry2 is considerably smaller than that in the wild type, indicating that 3B7N specifically interrupts cryptochrome function in the control of seedling development in a light-dependent manner. We demonstrated that 3B7N directly binds to CRY1 protein using an in vitro binding assay. These results suggest that 3B7N is a novel chemical that directly inhibits plant cryptochrome function by physical binding. The application of 3B7N can be used on other plants to study further the blue light mechanism and the genetic control of cryptochromes in the growth and development of plant species., (© The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

A wide range of biological processes exhibit circadian rhythm, enabling plants to adapt to the environmental day-night cycle. This rhythm is generated by the so-called 'circadian clock'. Although a number of genetic approaches have identified >25 clock-associated genes involved in the Arabidopsis clock mechanism, the molecular functions of a large part of these genes are not known. Recent comprehensive studies have revealed the molecular functions of several key clock-associated proteins. This progress has provided mechanistic insights into how key clock-associated proteins are integrated, and may help in understanding the essence of the clock's molecular mechanisms.

To investigate the mechanism of phytochrome action in vivo, NtPHYB, AtPHYB and phyD:green fluorescent protein (GFP) were overexpressed in Nicotiana plumbaginifolia and Arabidopsis thaliana. The expression of 35S:NtPHYB:GFP and 35S:AtPHYB:GFP complemented the tobacco hgl2 and Arabidopsis phyB-9 mutations, whereas the 35S:AtPHYD:GFP only rescued the hgl2 mutant. All three fusion proteins are transported into the nucleus in all genetic backgrounds. These data indicate that AtPHYD:GFP is biologically active and functions as the main red light receptor in transgenic tobacco, and establish an experimental system for the functional analysis of this elusive photoreceptor in vivo.

In Arabidopsis thaliana, a number of clock-associated protein components have been identified. Among them, CCA1 (CIRCADIAN CLOCK-ASSOCIATED 1)/LHY (LATE ELONGATED HYPOCOTYL) and TOC1 (TIMING OF CAB EXPRESSION 1) are believed to be the essential components of the central oscillator. CCA1 and LHY are homologous and partially redundant Myb-related DNA-binding proteins, whereas TOC1 is a member of a small family of proteins, designated as PSEUDO-RESPONSE REGULATOR. It is also believed that these two different types of clock components form an autoregulatory positive/negative feedback loop at the levels of transcription/translation that generates intrinsic rhythms. Nonetheless, it was not yet certain whether or not other PRR family members (PRR9, PRR7, PRR5 and PRR3) are implicated in clock function per se. Employing a set of prr9, prr7 and prr5 mutant alleles, here we established all possible single, double and triple prr mutants. They were examined extensively by comparing them with each other with regard to their phenotypes of circadian rhythms, photoperiodicity-dependent control of flowering time and photomorphogenic responses to red light during de-etiolation. Notably, the prr9 prr7 prr5 triple lesions in plants resulted in severe phenotypes: (i) arrhythmia in the continuous light conditions, and an anomalous phasing of diurnal oscillation of certain circadian-controlled genes even in the entrained light/dark cycle conditions; (ii) late flowering that was no longer sensitive to the photoperiodicity; and (iii) hyposensitivity (or blind) to red light in the photomorphogenic responses. The phenotypes of the single and double mutants were also characterized extensively, showing that they exhibited circadian-associated phenotypes characteristic for each. These results are discussed from the viewpoint that PRR9/PRR7/PRR5 together act as period-controlling factors, and they play overlapping and distinctive roles close to (or within) the central oscillator in which the relative, PRR1/TOC1, plays an essential role.

PHYTOCHROME-INTERACTING FACTOR-LIKE 6 (PIL6) is a member of the large family of basic/helix-loop-helix (bHLH) factors in Arabidopsis thaliana. This circadian-controlled transcription factor was previously suggested to interact with the clock component, TIMING OF CAB EXPRESSION 1 (TOC1). In this study, we isolated a loss-of-function mutant of PIL6, together with a transgenic line aberrantly expressing PIL6 in a manner independent of circadian rhythm. These mutant plants were simultaneously examined with special reference to circadian rhythm and light-signal transduction. The results suggested that PIL6 appears to be not directly involved in the clock function per se. However, the loss-of-function mutant (pil6-1) showed a remarkable phenotype in that it is hypersensitive to red light in seedling de-etiolation. This phenotype was similar to that observed for transgenic lines overexpressing TOC1 (or APRR1). Conversely, transgenic plants overexpressing PIL6 (PIL6-ox) are hyposensitive to red light under the same conditions. This phenotype was very similar to that observed for phyB mutants. The developmental morphologies of PIL6-ox, including the phenotype of early flowering, were also similar to those of phyB mutants. We propose that PIL6 acts as a negative regulator for a red light-mediated morphogenic response (e.g., elongation of hypocotyls in de-etiolation). Taken together, PIL6 might function at an interface between the circadian clock and red light-signal transduction pathways.

Allene oxide synthase (AOS) is a key enzyme for the biosynthesis of jasmonic acid (JA). We identified four AOS gene homologs, named OsAOS1-4, in the database of a japonica rice genome and cloned a full-length cDNA of OsAOS1. The analysis of deduced amino acid sequences indicated that only OsAOS1 has a chloroplast transit peptide among all the identified monocot AOSs including OsAOSs. We found that the transcripts of OsAOS1 and OsAOS4 are up-regulated by red and far-red light in seedling shoots. The response in OsAOS1 transcripts occurred rapidly and transiently, while the response in OsAOS4 transcripts was slower and more sustainable; the maximal enhancement was greater in OsAOS1 transcripts than in OsAOS4 transcripts. The transcript of OsAOS1 was also up-regulated transiently in response to wounding, as reported for dicot AOSs. No wound-induced enhancement occurred, however, in OsAOS4 transcripts. Our results also indicated that OsAOS1, responding to both light and wounding, is the most highly expressed of all the OsAOSs in seedling shoots. By using phyA mutants of rice, it was demonstrated that the photoregulation of the AOS transcript level is mediated by phytochrome. It is suggested that this transcriptional photoregulation participates in the phytochrome-mediated inhibition of rice coleoptile growth.