Yoichi Nakatani

Enzymic determination of L-lysine in biological materials.

Abstract A simple and rapid method for the determination of l -lysine is presented. The method measures the amount of NADH oxidized on incubation of a lysine-containing sample with α-ketoglutarate and saccharopine dehydrogenase. A strict substrate specificity of the enzyme and the equilibrium of the reaction which is in favor of saccharopine formation make possible the specific determination of l -lysine to be done in crude biological materials.

Blue light-induced conformational changes in a light-regulated transcription factor, aureochrome-1.

Aureochrome-1 (AUREO1) is a blue light (BL) receptor that mediates the branching response in the stramenopile alga, Vaucheria frigida. AUREO1 harbors a basic leucine zipper (bZIP) domain at the N-terminus and a light-oxygen-voltage-sensing (LOV) domain within the C-terminal region, and has been suggested to function as a light-regulated transcription factor. To understand the molecular mechanism of AUREO1, we have prepared three recombinant proteins: a full-length AUREO1 (FL), an N-terminal truncated construct containing bZIP and LOV (ZL) and a LOV-only (LOV) construct. The constructs showed the same absorption and fluorescent spectra in the dark state and underwent the characteristic cyclic reaction as previously observed in LOV domains upon BL excitation. FL and ZL bound to DNA in a sequence-specific manner. BL appeared to induce a shift of the α-helical structure of the LOV domain to a β-sheet structure, but did not alter the hydrodynamic radius (R(H)) of this domain. ZL formed a dimer possibly through disulfide linkages in the bZIP and the linker region between bZIP and LOV. BL induced an approximately 5% increase in the R(H) of ZL, although its secondary structure was unchanged. These results support a schema where BL-induced changes in the LOV domain may cause conformational changes in the bZIP and/or the linker of a dimeric ZL molecule. Since a 5% increase of the R(H) was also observed with the FL construct, BL may induce global conformational changes similar to those observed for ZL, and formation of the FL dimer may facilitate DNA binding.

Blue Light-induced Dimerization of Monomeric Aureochrome-1 Enhances Its Affinity for the Target Sequence

Background: Aureochromes in stramenopiles are thought to function as light-regulated transcription factors, although the molecular mechanism is unknown. Results: Monomeric AUREO1 is present in reduced conditions and undergoes dimerization upon illumination. Conclusion: Blue light-induced dimerization enhances the affinity for the target sequence. Significance: AUREO1 is useful for understanding the blue light responses of stramenopiles, and for optogenetics and biophysical analyses. Aureochrome-1 (AUREO1) is a blue light (BL) receptor that mediates the branching response in stramenopile alga, Vaucheria frigida. AUREO1 contains a basic leucine zipper (bZIP) domain in the central region and a light-oxygen-voltage sensing (LOV) domain at the C terminus, and has been suggested to function as a light-regulated transcription factor. We have previously reported that preparations of recombinant AUREO1 contained the complete coding sequence (full-length, FL) and N-terminal truncated protein (ZL) containing bZIP and LOV domains, and suggested that wild-type ZL (ZLwt2) was in a dimer form with intermolecular disulfide linkages at Cys162 and Cys182 (Hisatomi, O., Takeuchi, K., Zikihara, K., Ookubo, Y., Nakatani, Y., Takahashi, F., Tokutomi, S., and Kataoka, H. (2013) Plant Cell Physiol. 54, 93–106). In the present study, we report the photoreactions, oligomeric structures, and DNA binding of monomeric cysteine to serine-mutated ZL (ZLC2S), DTT-treated ZL (DTT-ZL), and FL (DTT-FL). Recombinant AUREO1 showed similar spectral properties and dark regeneration kinetics to those of dimeric ZLwt2. Dynamic light scattering and size exclusion chromatography revealed that ZLC2S and DTT-ZL were monomeric in the dark state. Dissociation of intermolecular disulfide bonds of ZLwt2 was in equilibrium with a midpoint oxidation-redox potential of approximately −245 ± 15 mV. BL induced the dimerization of monomeric ZL, which subsequently increased its affinity for the target sequence. Also, DTT-FL was monomeric in the dark state and underwent BL-induced dimerization, which led to formation of the FL2·DNA complex. Taken together, our results suggest that monomeric AUREO1 is present in vivo, with dimerization playing a key role in its role as a BL-regulated transcription factor.

α-Aminoadipate aminotransferase of rat liver mitochondria

Abstract α-Aminoadipate aminotransferase was partially purified from rat liver mitochondria. The enzyme catalyzes a reversible transamination between α-aminoadipate and α-ketoglutarate. The aminotransferase has rather loosely bound coenzyme; a prolonged dialysis of enzyme against phosphate buffer resulted in an almost complete loss of its catalytic activity. The enzymic activity of the apoenzyme was largely restored by either pyridoxal or pyridoxamine phosphate. The equilibrium constant of the reaction was about 1.32 at pH 7.5 and at 37°, and the Michaelis constants for α-aminoadipate, glutamate, α-ketoadipate, and α-ketoglutarate were 9.0, 5.0, 0.5 and 1.3 mM, respectively. α-Aminoadipate aminotransferase has a strict substrate specificity. In trans-amination with α-ketoglutarate, α-aminopimelate and norleucine were about 14% and 15% active in place of α-aminoadipate, whereas the other amino acids tested were inert as substrates.

Molecular Mechanism of Photozipper, a Light-Regulated Dimerizing Module Consisting of the bZIP and LOV Domains of Aureochrome-1

Aureochrome-1 (AUREO1) is a blue light (BL) receptor responsible for the BL-induced blanching of a stramenopile alga, Vaucheria frigida. The AUREO1 protein contains a central basic region/leucine zipper (bZIP) domain, and a C-terminal light-oxygen-voltage-sensing (LOV) domain. BL induces the dimerization of monomeric AUREO1, which subsequently increases the affinity of this transcription factor for its target DNA [Hisatomi, O., et al. (2014) J. Biol. Chem. 289, 17379-17391]. We constructed a synthetic gene encoding N-terminally truncated monomeric AUREO1 (designated Photozipper) to elucidate the molecular mechanism of this BL-regulated transcription factor and to develop it as an optogenetic tool. In this study, four different Photozipper (PZ) protein constructs were prepared comprising different N-terminal truncations. The monomer-dimer equilibria of the PZ constructs were investigated in the dark and light states. Dynamic light scattering and size-exclusion chromatography analyses revealed that the apparent dissociation constants of PZ dimers with and without the ZIP region were ~100 and 30 μM, respectively, indicating that the ZIP region stabilized the monomeric form in the dark state. In the light state, fluorescence resonance energy transfer analyses demonstrated that deletion of the ZIP region increased the dissociation constant from ~0.15 to 0.6 μM, suggesting that intermolecular LOV-LOV and ZIP-ZIP interactions stabilized the dimeric forms. Our results suggest that synergistic interactions between the LOV and bZIP domains stabilize the monomeric form in the dark state and the dimeric form in the light state, which possibly contributes to the function of PZ as a BL-regulated molecular switch.

Time-Resolved Detection of Light-Induced Dimerization of Monomeric Aureochrome-1 and Change in Affinity for DNA.

Aureochrome (Aureo) is a recently discovered blue light sensor protein initially from Vaucheria frigida, in which it controls blue light-dependent branch formation and/or development of a sex organ by a light-dependent change in the affinity for DNA. Although photochemical reactions of Aureo-LOV (LOV is a C-terminal light-oxygen-voltage domain) and the N-terminal truncated construct containing a bZIP (N-terminal basic leucine zipper domain) and a LOV domain have previously been reported, the reaction kinetics of the change in affinity for DNA have never been elucidated. The reactions of Aureo where the cysteines are replaced by serines (AureoCS) as well as the kinetics of the change in affinity for a target DNA are investigated in the time-domain. The dimerization rate constant is obtained as 2.8 × 10(4) M(-1) s(-1), which suggests that the photoinduced dimerization occurs in the LOV domain and the bZIP domain dimerizes using the interaction with DNA. Surprisingly, binding with the target DNA is completed very quickly, 7.7 × 10(4) M(-1) s(-1), which is faster than the protein dimerization rate. It is proposed that the nonspecific electrostatic interaction, which is observed as a weak binding with DNA, may play a role in the efficient searching for the target sequence within the DNA.

Quantitative analyses of the equilibria among DNA complexes of a blue-light-regulated bZIP module, Photozipper

Aureochrome1 is a blue-light-receptor protein identified in a stramenopile alga, Vaucheria frigida. Photozipper (PZ) is an N-terminally truncated, monomeric, V. frigida aureochrome1 fragment containing a basic leucine zipper (bZIP) domain and a light–oxygen–voltage (LOV)-sensing domain. PZ dimerizes upon photoexcitation and consequently increases its affinity for the target sequence. In the present study, to understand the equilibria among DNA complexes of PZ, DNA binding by PZ and mutational variants was quantitatively investigated by electrophoretic-mobility-shift assay and fluorescence-correlation spectroscopy in the dark and light states. DNA binding by PZ was sequence-specific and light-dependent. The half-maximal effective concentration of PZ for binding to the target DNA sequence was ~40 nM in the light, which was >10-fold less than the value in the dark. By contrast, the dimeric PZ-S2C variant (with intermolecular disulfide bonds) had higher affinity for the target sequence, with dissociation constants of ~4 nM, irrespective of the light conditions. Substitutions of Glu159 and Lys164 in the leucine zipper region decreased the affinity of PZ for the target sequence, especially in the light, suggesting that these residues form inter-helical salt bridges between leucine zipper regions, stabilizing the dimer–DNA complex. Our quantitative analyses of the equilibria in PZ–DNA-complex formation suggest that the blue-light-induced dimerization of LOV domains and coiled-coil formation by leucine zipper regions are the primary determinants of the affinity of PZ for the target sequence.