Daisaku Ohta

Insect Cell Expression of Recombinant Imidazoleglycerolphosphate Dehydratase of Arabidopsis and Wheat and Inhibition by Triazole Herbicides

Imidazoleglycerolphosphate dehydratase (IGPD; EC 4.2.1.19), which is involved in the histidine biosynthetic pathway of Arabidopsis thaliana and wheat (Triticum aestivum), has been expressed in insect cells using the baculovirus expression vector system. N-terminal amino acid sequencing indicated that recombinant IGPDs (rIGPDs) were produced as mature forms via nonspecific proteolytic cleavages in the putative transit peptide region. The wheat rIGPD contained one Mn atom per subunit, and the Mn was involved in the assembly of the subunits to form active IGPDs. Protein-blotting analysis, using antibodies raised against the wheat rIGPD, indicated that IGPD was located in the chloroplasts of wheat. The rIGPDs of Arabidopsis and wheat, which were 86% identical in their primary structures deduced from the cDNAs, exhibited similar properties in terms of the molecular mass, pH optimum, and the Km for the substrate, imidazoleglycerolphosphate. However, the nonselective herbicides 3-amino-1,2,4-triazole and a newly synthesized triazole [(1R*, 3R*)-[3-hydroxy-3-(2H-[1,2,4]triazole-3-yl)-cyclohexyl]-phosphonic acid], inhibited Arabidopsis and wheat IGPDs in a mixed-type and a competitive manner, respectively.

Isolation and characterization of mutations affecting expression of the Δ9‐ fatty acid desaturase gene, OLE1, in Saccharomyces cerevisiae

Expression of the Δ9‐ fatty acid desaturase gene, OLE1, of Saccharomyces cerevisiae is negatively regulated transcriptionally and post‐transcriptionally by unsaturated fatty acids. In order to isolate mutants exhibiting irregulation of OLE1 expression, we constructed an OLE1p–PHO5 fusion gene as a reporter consisting of the PHO5 gene encoding repressible acid phosphatase (rAPase) under the control of the OLE1 promoter (OLE1p). By EMS mutagenesis, we isolated three classes of mutants, pfo1, pfo2 and pfo3 (

Isolation and Characterization of cDNAs Encoding Imidazoleglycerolphosphate Dehydratase from Arabidopsis thaliana

cDNA clones encoding imidazoleglycerolphosphate dehydratase (IGPD; EC 4.2.1.19) from Arabidopsis thaliana were isolated by complementation of a bacterial auxotroph. The predicted primary translation product shared significant identity with the corresponding sequences from bacteria and fungi. As in yeast, the plant enzyme is monofunctional, lacking the histidinol phosphatase activity present in the Escherichia coli protein. IGPD mRNA was present in major organs at all developmental stages assayed. The Arabidopsis genome appears to contain two genes encoding this enzyme, based on DNA gel blot and polymerase chain reaction analysis.

Expression and characterization of a rabbit liver cytochrome P450 belonging to P450IIB subfamily with the aid of the baculovirus expression vector system

Using baculovirus a cDNA for cytochrome P450 (P450F1) belonging to rabbit P450IIB subfamily was expressed in Spodoptera frugiperda cells, where P450F1 was located on electron-dense structures (derived from the endoplasmic reticulum) present in both the cytoplasm and nucleus. Partially purified P450F1 exhibited absorption spectra similar to those of P450(1), the major phenobarbital-inducible form in rabbit liver. Like P450(1), P450F1 could oxidize aminopyrine, benzphetamine, 7-ethoxycoumarin, 1-nitropropane, and 2-nitropropane, though its activities toward benzphetamine and 7-ethoxycoumarin were about 50 and 5%, respectively, of those of P450(1). It is concluded that the members of P450IIB subfamily can act on a variety of xenobiotics, although substrate preferences are different among them.

Theoretical evidence of the existence of a diazafulvene intermediate in the reaction pathway of imidazoleglycerol phosphate dehydratase: design of a novel and potent heterocycle structure for the inhibitor on the basis of the electronic structure-activity relationship study

The reaction mechanism of imidazoleglycerol phosphate dehydratase has not yet been clearly revealed. Structural comparison between inhibitors and the substrate IGP implicates that the reaction involves a diazafulvene intermediate. Here, we present evidence to support this hypothesis by investigating the electronic structure-enzyme inhibitory activity relationship on inhibitors with different heterocycles using 6-31G** level theory of the ab initio molecular orbital method. The calculation results showed that potent inhibitors can be distinguished from weak ones by the atomic charge density and by the energy levels of the highest occupied lone-pair orbital on the nitrogen atoms in the heterocycles. Furthermore, very good correlations (r2=0.8-0.9) were found between the charge density on the nitrogen atom and the inhibitory activity. It was also revealed that the diazafulvene is electronically similar to the potent inhibitors. Thus, these results strongly suggest the existence of the diazafulvene as an intermediate possessing tight-binding affinity to the enzyme. Based on the electronic structural similarity between the potent inhibitors and the proposed intermediate, a novel heterocycle was designed and predicted its inhibitory activity prior to the synthesis. Then, activity of synthesized inhibitors showed excellent agreement with this prediction. Hence, from the theoretical studies and experimental results, we conclude to obtain evidence of the hypothesis that the enzyme reaction proceeds via the diazafulvene intermediate.

Molecular cloning and characterization of the gene encoding N¢-((5¢-phosphoribosyl)-formimino)-5-aminoimidazole-4-carboxamide ribonucleotide (BBM II) isomerase from Arabidopsis thaliana

Abstract We have isolated an Arabidopsis BBM II isomerase cDNA from an Arabidopsis cDNA library, by means of functional complementation of the E. coli hisA mutant strain HfrG6. The isolated cDNA encodes a polypeptide of 304 amino acids with a calculated molecular weight of 33u2004363. Sequence comparison with the HIS6 proteins of yeasts revealed that Arabidopsis BBM II isomerase contains an N-terminal extension of approximately 40 amino acids that shows the general properties of chloroplast transit peptides. This finding is consistent with the localization of other histidine biosynthetic enzymes, such as imidazoleglycerolphosphate dehydratase and histidinol dehydrogenase, in the chloroplasts in higher plants. The primary structure of the mature protein was 50% and 42% identical, respectively, to the HIS6 proteins of Schizosaccharomyces pombe and Saccharomyces cerevisiae, respectively, while no prominent sequence similarity to the bacterial BBM II isomerase was found. That the isolated Arabidopsis cDNA actually encodes a functionally active BBM II isomerase activity was confirmed in an in vitro enzyme assay using a crude extract prepared from strain HfrG6 transformed with the Arabidopsis BBM II isomerase cDNA.

Overexpression of plant histidinol dehydrogenase using a baculovirus expression vector system

A cDNA encoding cabbage histidinol dehydrogenase, including the chloroplast transit peptide sequence, was overexpressed using a baculovirus expression vector system. The maximum level of the expression of histidinol dehydrogenase was reached 5 days after infection of the insect cells. Two forms of recombinant histidinol dehydrogenase with molecular masses of 53 and 52 kDa, respectively, were obtained by a one-step purification from the cell homogenate. Compared with the 52-kDa form, the 53-kDa form contained 10 additional amino acids at the N-terminus derived from the transit peptide. By incubating the cell homogenate for 2 h at 30 degrees C, the 53-kDa form could be completely converted to the 52-kDa form. This conversion was blocked by leupeptin. Eighty percent of the converted 52-kDa form had Cys at position 31 at the N-terminal amino acid and the rest had Met 33. Kinetic properties of the recombinant enzyme were virtually identical to those of histidinol dehydrogenase isolated from cabbage plants. The overexpression of recombinant cabbage histidinol dehydrogenase in insect cells, the proteolytic processing of the preprotein next to the N-terminus (compared to the mature cabbage enzyme), and its easy purification allow the preparation of large amounts of the active enzyme for structural and functional studies.

Computational modeling of a binding conformation of the intermediate L-histidinal to histidinol dehydrogenase.

Histidinol dehydrogenase (HDH) is one of the enzymes involved in the L-histidine biosynthesis pathway. HDH is a dimer that contains one Zn2+ ion in each identical subunit. In this study, we predicted a possible binding conformation of the intermediate L-histidinal, which is experimentally not known, using a computational modeling method and three potent HDH inhibitors whose structures are similar to that of L-histidinal. At first, a set of the most probable active conformations of the potent inhibitors was determined using two different pharmacophore mapping techniques, the active analogue approach and the distance comparison method. From the most probable active conformations of the three potent inhibitors, the common parts of the L-histidinal structure were extracted and refined by energy minimization to obtain the binding conformation of L-histidinal. This predicted conformation of L-histidinal agrees with an experimentally determined conformation of L-histidine in a single crystal, suggesting that it is an experimentally acceptable conformation. The capability in this conformation to coordinate a Zn2+ ion was examined by comparing the spatial relative geometry of its functional groups with those of ligands that coordinate with a Zn2+ ion in Zn proteins of the Protein Data Bank. This comparison supported our predicted conformation.

Effect of excess cadmium ion on the metal binding site of cabbage histidinol dehydrogenase studied by 113Cd-NMR spectroscopy

The enzymatic reaction of histidinol dehydrogenase (HDH) was stimulated by about maximally 75% on the addition of Cd2+ ion to the reaction mixture. 113Cd‐substituted HDH in the presence of excess Cd2+ has been studied by 113Cd‐NMR. 113Cd2+ less than 1 equiv. per subunit preferentially binds to the catalytic metal binding site of the apoenzyme. Further addition of the metal ions causes the structural change of the enzyme including the catalytic metal binding site. HDH takes at least three discernible states, which may correspond to the more or less active forms of the enzyme induced by metal ions.

A CoMFA analysis with conformational propensity: An attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method

CoMFA analysis, a widely used 3D-QSAR method, has limitations to handle a set of SAR data containing diverse conformational flexibility since it does not explicitly include the conformational entropic effects into the analysis. Here, we present an attempt to incorporate the conformational entropy effects of a molecule into a 3D-QSAR analysis. Our attempt is based on the assumption that the conformational entropic loss of a ligand upon making a ligand-receptor complex is small if the ligand in an unbound state has a conformational propensity to adopt an active conformation in a complex state. For a QSAR analysis, this assumption was interpreted as follows: a potent ligand should have a higher conformational propensity to adopt an `active-conformation-like structure in an unbound state than an inactive one. The conformational propensity value was defined as the populational ratio, Nactive/Nstable, of the number of energetically stable conformers, Nstable, to the number of `active-conformation-like structures, Nactive. The latter number was calculated by counting the number of conformers that satisfied the structural parameters deduced from the active conformation. A set of SAR data of imidazoleglycerol phosphate dehydratase inhibitors containing 20 molecules with different conformational flexibility was used as a training set for developing a 3D structure-activity relationship by a CoMFA analysis with the conformational propensity value. This resulted in a cross-validated squared correlation coefficient of the CoMFA model with the conformational propensity value (R2cross = 0.640) higher than that of the standard CoMFA model (R2cross = 0.431). Then we evaluated the quality of the CoMFA models by predicting the inhibitory activity for a new molecule.