Katsushi Manabe

Identification of Arabidopsis Genes Regulated by High Light–Stress Using cDNA Microarray¶

Abstract In plants, excess light has the potential to damage the photosynthetic apparatus. The damage is caused in part by reactive oxygen species (ROS) generated by electrons leaking from the photosynthetic electron transport system. To investigate the mechanisms equipped in higher plants to reduce high light (HL) stress, we surveyed the response of 7000 Arabidopsis genes to HL, taking advantage of the recently developed microarray technology. Our analysis revealed that 110 genes had a positive response to a 3 h treatment at a light intensity of 150 W m−2. In addition to the scavenging enzymes of ROS, the genes involved in biosynthesis of lignins and flavonoids are activated by HL and actually resulted in increased accumulation of lignins and anthocyanins. Comparing the HL-responsive genes with drought-inducible genes identified with the same microarray system revealed a dense overlap between HL- and drought-inducible genes. In addition, we have identified 10 genes that showed upregulation by HL, drought, cold and also salt stress. These genes include RD29A, ERD7, ERD10, KIN1, LEA14 and COR15a, most of which are thought to be involved in the protection of cellular components.

Arabidopsis transcriptional regulation by light stress via hydrogen peroxide‐dependent and ‐independent pathways

Background High (intense) light stress causes the formation of oxygen radicals in chloroplasts and has the potential to damage them. However, plants are able to respond to this stress and protect the chloroplasts by various means, including transcriptional regulation in the nucleus. Although the corresponding signalling pathway is largely unknown, the high light response in the expression of the Arabidopsis APX2 gene is reported to be mediated by hydrogen peroxide.

Expression of the circadian clock-related gene pex in cyanobacteria increases in darkness and is required to delay the clock.

The time measurement system of the unicellular cyanobacterium Synechococcus elongatus PCC 7942 is analogous to the circadian clock of eukaryotic cells. Circadian clock-related genes have been identified in this strain. The clock-related gene pex is thought to maintain the normal clock period because constitutive transcription or deficiency of this gene causes respectively longer (~28 h) or shorter (~24 h) circadian periods than that of the wild type (~25 h). Here, the authors report other properties of pex in the circadian system. Levels of pex mRNA increased significantly in a 12-h exposure to darkness. Western blotting with a GST-Pex antibody revealed a 13.5-kDa protein band in wild-type cells that were incubated in the dark, while this protein was not detected in pex-deficient mutant cells. Therefore, the molecular weight of the Pex protein appears to be 13.5 kDa in vivo. The PadR domain, which is conserved among DNA-binding transcription factors in lactobacilli, was found in Pex. In the pex mutant, several 12-h light/12-h dark cycles reset the phase of the clock by 3 h earlier (phase advance) compared to wild-type cells. The degree of the advance in the pex mutant was proportional to the number of exposed light-dark cycles. In addition, ectopic induction of pex with an inducible Escherichia coli promoter, Ptrc, delayed the phase in the examined recombinant cells by 2.5 h (phase delay) compared to control cells. These results suggest that the dark-responsive gene expression of pex delays the circadian clock under daily light-dark cycles.

Equal-quantum Action Spectra Indicate Fluence-rate–selective Action of Multiple Photoreceptors for Photomovement of the Thermophilic Cyanobacterium Synechococcus elongatus¶

Unicellular thermophilic cyanobacterium Synechococcus elongatus displayed phototaxis on agar plate at 55°C. Equal‐quantum action spectra for phototactic migration were determined at various fluence rates using the Okazaki Large Spectrograph as the light source. The shapes of the action spectra drastically changed depending on the fluence rate of the unilateral monochromatic irradiation: at a low fluence rate (3 μmol/m2/s), only lights in the red region had significant effect; at a medium fluence rate (10 μmol/m2/s), four major action peaks were observed at 530 nm (green), 570 nm (yellow), 640 nm (red) and 680 nm (red). At high fluence rates (30–90 μmol/m2/s), the former two peaks remained, while red peaks at 640 nm and 680 nm disappeared and, interestingly, an action peak around 700–740 nm (far‐red) newly appeared. These results indicate that two or more distinct photoreceptors are involved in the phototaxis and that suitable photoreceptors are selectively active in response to the stimulus of light fluence rates. Far‐red or red background lights irradiated vertically from above drastically inhibited phototaxis toward red light or far‐red light, respectively. These results indicate involvement of some phytochrome(s).

Two-dimensional gel electrophoresis of the membrane-bound protein complexes, including photosystem I, of thylakoid membranes in the presence of sodium oligooxyethylene alkyl ether sulfate/dimethyl dodecylamine oxide and sodium dodecyl sulfate

Two-dimensional polyacrylamide gel electrophoresis (PAGE), using a mixture of sodium oligooxyethylene alkyl ether sulfate and dimethyl dodecylamine oxide as detergents (AES-DDAO mixture) in the first dimension and sodium dodecyl sulfate (SDS) in the second dimension, was developed and applied to an analysis of the photosystem I (PS I) complex in thylakoid membranes prepared from spinach chloroplasts. When thylakoid membranes of chloroplasts were solubilized directly in the AES-DDAO mixture and subjected to PAGE in the presence of these detergents as the first dimension, some protein complexes containing chlorophyll were observed. The protein components in these complexes separated into an array of polypeptide spots when the strip of gel after PAGE in the first dimension was subjected to PAGE in the presence of SDS as the second dimension. The main band of protein which separated in the first dimension was demonstrated to be the PS I complex. This complex retained the intrinsic photochemical activity of P700 even after it was subjected to one-dimensional PAGE. These results suggest that certain protein complexes can be separated, with the maintenance of their original structures, by electrophoresis in the presence of the AES-DDAO mixture, and this method appears to have valuable potential for analysis of the components of membrane-bound protein complexes.

The direct hydrolysis of proteins containing tryptophanon polyvinylidene difluoride membranes by mercaptoethanesulfonic acid in the vapor phase

A procedure for the amino acid analysis of polypeptides that contain tryptophan on polyvinylidene difluoride membranes is described. Lysozyme, carbonic anhydrase, phytochrome, and ovalbumin were tested. The protein, which was separated from others by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, was blotted from the gel onto a polyvinylidene difluoride membrane and directly hydrolyzed by 3 N mercaptoethanesulfonic acid vapor in a vacuum at 176 degrees C for 25 min. The hydrolysate was extracted with 0.1 N HCl and 30% methanol and used for amino acid analysis. The tested proteins were adequately hydrolyzed, and the recovery of tryptophan was very efficient.

Spectral properties and photoactivities of intermediates of photoconversion from the red-light-absorbing to far-red-light-absorbing form of pea phytochrome

Abstract The pathway for the phototransformation of the red-light-absorbing (Pr) to the far-red-light-absorbing (Pfr) form of native phytochrome A from pea was investigated by low temperature spectrophotometry. Four intermediates between Pr and Pfr were recognized. The first intermediate (lumi-R) was stable below −100°C. The other intermediates and Pfr appeared during warming of lumi-R to −80 °C (meta-Ra), −40 °C (meta-Rb′), −20 °C (meta-Rc) and 0 °C (Pfr). Each intermediate (lumi-R, meta-Ra and meta-Rc) and Pr was photointerconvertible as a two-component system at the temperature at which the intermediate had initially appeared. Meta-Rb′ is also photoconvertible to Pr. Prolonged red light irradiation of meta-Rb′ at −40 °C resulted in appearance of another intermediate (meta-Rb).

CmpR is Important for Circadian Phasing and Cell Growth

In the cyanobacterium Synechococcus elongatus PCC 7942, the circadian clock entrains to a daily light/dark cycle. The transcription factor Pex is abundant under dark conditions and represses kaiA transcription to fine-tune the KaiC-based core circadian oscillator. The transcription of pex also increases during exposure to darkness; however, its mechanism is unknown. We performed a molecular genetic study by constructing a pex expression bioluminescent reporter and screening for brightly luminescent mutants by random insertion of a drug resistance gene cassette in the reporter genome. One mutant contained an insertion of an antibiotic resistance cassette in the cmpR locus, a transcriptional regulator of inorganic carbon concentration. Insertions of the cassette in the remaining two mutant genomes were in the genes encoding flavodoxin and a putative partner of an ABC transporter with unknown function (ycf22). We further analyzed the cmpR mutant to examine whether CmpR directly or indirectly targeted pex expression. In the cmpR mutant, the pex mRNA level was 1.8-fold that of the wild type, and its circadian peak phase in bioluminescence rhythm occurred 5 h later. Moreover, a high-light stress phenotype was present in the colony. The abnormalities were complemented by ectopic induction of the native gene. However, the cmpR/pex double mutation partly suppressed the phase abnormality (2.5 h). In vitro DNA binding analysis of CmpR showed positive binding to the psbAII promoter, but not to any pex DNA. We postulate that the phenotypes of cmpR-deficient cells were attributable mainly to a feeble metabolic and/or redox status.

ULTRAVIOLET RESONANCE RAMAN SPECTRA OF PHYTOCHROME: A COMPARISON OF THE ENVIRONMENTS OF TRYPTOPHAN SIDE CHAINS BETWEEN RED LIGHT‐ABSORBING AND FAR‐RED LIGHT‐ABSORBING FORMS

Ultraviolet resonance Raman spectra of phytochrome in the red light‐absorbing form (Pr) and the far‐red light‐absorbing form (Pfr) are reported. The spectra excited at 240‐nm provide structural information about the protein part of phytochrome. The protein contains only a very small amount of β‐sheet structure and most of the tyrosine side chains are located in hydrophobic environments. Indole rings of tryptophan (Trp) interact with neighboring groups in the Pr form and these interactions become weaker with the conversion from Pr to Pfr. Some Trp side chains of Pfr are surrounded by aliphatic groups but such is not the case in Pr. These changes in the environment occur at the same time as changes in orientation of Trp side chains. Our observations suggest that interactions between Trp residues and the tetrapyrrolic chromophore occur in the Pr form and that the strength of these interactions diminishes in the Pfr form.

The Structure and Function of Phytochrome A : the Roles of the Entire Molecule and of Its Various Parts

Phytochrome A is readily cleavable by proteolytic agents to yield an amino-terminal fragment of 66 kilodalton (kDa), which consists of residues 1 to approximately 600, and a dimer of the carboxy-terminal 55-kDa fragment, from residue 600 or so to the carboxyl terminus. The former domain, carrying the tetrapyrrole chromophore, has been studied extensively because of its photoactivity, while less attention has been paid to the non-chromophoric portion until quite recently. However, the evidence gathered to date suggests that this domain is also of great improtance. We present here a review of the structure and the biochemical and physiological functions of the two domains, of parts of these domains, and of the cooperation between them.