A role of nitrite reductase (NirBD) for NO homeostatic regulation in Streptomyces coelicolor A3(2).

Although nitric oxide (NO) is an important signaling molecule in bacteria and higher organisms, excessive intracellular NO is highly reactive and dangerous. Therefore, living cells need strict regulation systems for cellular NO homeostasis. Recently, we discovered that Streptomyces coelicolor A3(2) retains the nitrogen oxide cycle (NO3-→NO2-→NO→NO3-) and nitrite removal system. The nitrogen oxide cycle regulates cellular NO levels, thereby controlling secondary metabolism initiation (red-pigmented antibiotic, RED production) and morphological differentiation. Nitrite induces gene expression in neighboring cells, suggesting another role for this cycle as a producer of transmittable intercellular communication molecules. Here, we demonstrated that ammonium-producing nitrite reductase (NirBD) is involved in regulating NO homeostasis in S. coelicolor A3(2). NirBD was constitutively produced in culture independently of GlnR, a known transcriptional factor. NirBD cleared the accumulated nitrite from the medium. Nir deletion mutants showed increased NO-dependent gene expression at later culture stages, whereas the wild-type M145 showed decreased expression, suggesting that high NO concentration was maintained in the mutant. Moreover, the nir deletion mutant produced more RED than that produced by the wild-type M145. These results suggest that NO2- removal by NirBD is important to regulate NO homeostasis and to complete NO signaling in S. coelicolor.

Nitrogen oxide cycle regulates nitric oxide levels and bacterial cell signaling.

Nitric oxide (NO) signaling controls various metabolic pathways in bacteria and higher eukaryotes. Cellular enzymes synthesize and detoxify NO; however, a mechanism that controls its cellular homeostasis has not been identified. Here, we found a nitrogen oxide cycle involving nitrate reductase (Nar) and the NO dioxygenase flavohemoglobin (Fhb), that facilitate inter-conversion of nitrate, nitrite, and NO in the actinobacterium Streptomyces coelicolor. This cycle regulates cellular NO levels, bacterial antibiotic production, and morphological differentiation. NO down-regulates Nar and up-regulates Fhb gene expression via the NO-dependent transcriptional factors DevSR and NsrR, respectively, which are involved in the auto-regulation mechanism of intracellular NO levels. Nitrite generated by the NO cycles induces gene expression in neighboring cells, indicating an additional role of the cycle as a producer of a transmittable inter-cellular communication molecule.

Crystal structures of the ternary complex of APH(4)-Ia/Hph with hygromycin B and an ATP analog using a thermostable mutant.

Aminoglycoside 4-phosphotransferase-Ia (APH(4)-Ia)/Hygromycin B phosphotransferase (Hph) inactivates the aminoglycoside antibiotic hygromycin B (hygB) via phosphorylation. The crystal structure of the binary complex of APH(4)-Ia with hygB was recently reported. To characterize substrate recognition by the enzyme, we determined the crystal structure of the ternary complex of non-hydrolyzable ATP analog AMP-PNP and hygB with wild-type, thermostable Hph mutant Hph5, and apo-mutant enzyme forms. The comparison between the ternary complex and apo structures revealed that Hph undergoes domain movement upon binding of AMP-PNP and hygB. This was about half amount of the case of APH(9)-Ia. We also determined the crystal structures of mutants in which the conserved, catalytically important residues Asp198 and Asn203, and the non-conserved Asn202, were converted to Ala, revealing the importance of Asn202 for catalysis. Hph5 contains five amino acid substitutions that alter its thermostability by 16°C; its structure revealed that 4/5 mutations in Hph5 are located in the hydrophobic core and appear to increase thermostability by strengthening hydrophobic interactions.

Contact sex pheromone components of the seed beetle, Callosobruchus analis (F.).

Callosobruchus analis (Coleoptera: Chrysomelidae: Bruchinae), found throughout tropical Asia and Africa, is a pest of stored legumes. Previous work has shown that females of this species produce a contact sex pheromone that elicits copulatory behavior in males. Comparisons of copulatory activity between any two of four congeneric species suggest that the contact sex pheromones are species specific. In laboratory bioassays, male C. analis exhibited copulatory behavior to a female dummy to which a crude extract of virgin females was applied. The extract had been collected by a filter paper method and was purified by acid-base partition and chromatographic techniques. Gas chromatography-mass spectrometry (GC-MS) analyses of active fractions revealed that the active compounds were 2,6-dimethyloctane-1,8-dioic acid (1) and callosobruchusic acid, (E)-3,7-dimethyl-2-octene-1,8-dioic acid (2), previously identified as contact sex pheromones of Callosobruchus maculatus (F.) and C. chinensis (L.), respectively. The stereoisomeric and chemical compositions were determined by the 2D-HPLC-Ohrui-Akasaka method as (2S,6R)-1:(S)-2=1.8:1, which meant that both compounds in C. analis were stereochemically pure, unlike the case of C. maculatus and C. chinensis. An examination of the influence of synthetic pheromone compounds on male copulatory activity revealed that (2S,6R)-1 is the main component, and that (S)-2 has an additive effect. In the examination of the stereochemistry-activity relationship, no copulatory behavior was elicited by (2R,6S)-1, and, furthermore, the enantiomer significantly masked the pheromonal activity of (2S,6R)-1. Glass rod dummy assays also suggested the presence of synergists. These results could elucidate the specificity of mate recognition in C. analis.

2,3-Dihydrohomofarnesal: female sex attractant pheromone component of Callosobruchus rhodesianus (Pic).

Callosobruchus rhodesianus (Pic) (Coleoptera: Chrysomelidae: Bruchinae) is a pest of stored legumes through the Afro-tropical region. In laboratory bioassays, males of C. rhodesianus were attracted to volatiles collected from virgin females. Collections were purified by various chromatographic techniques, and the biologically active component isolated using gas chromatographic-electroantennographic detection analysis. Gas chromatography-mass spectrometry and NMR analyses suggested that the active compound was 2,3-dihydrohomofarnesal, i.e., 7-ethyl-3,11-dimethyl-6,10-dodecadienal. The structure was confirmed by non-stereoselective and enantioselective total synthesis. Using chiral gas chromatography, the absolute configuration of the natural compound was confirmed as (3S,6E)-7-ethyl-3,11-dimethyl-6,10-dodecadienal. Y-tube olfactomter assays showed that only the (S)-enantiomer attracted males of C. rhodesianus. The (R)-enantiomer and racemate did not attract males, suggesting that the (R)-enantiomer inhibits the activity of the natural compound. In combination with previous reports about sex attractant pheromones of congeners, we suggest that a saltational shift of the pheromone structure arose within the genus Callosobruchus.

Crystal structure of 1-deoxy-d-xylulose 5-phosphate reductoisomerase from the hyperthermophile Thermotoga maritima for insights into the coordination of conformational changes and an inhibitor binding.

Isopentenyl diphosphate is a precursor of various isoprenoids and is produced by the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway in plastids of plants, protozoa and many eubacteria. A key enzyme in the MEP pathway, 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), has been shown to be the target of fosmidomycin, which works as an antimalarial, antibacterial and herbicidal compound. In this paper, we report studies of kinetics and the crystal structures of the thermostable DXR from the hyperthermophile Thermotoga maritima. Unlike the mesophilic DXRs, Thermotoga DXR (tDXR) showed activity only with Mg(2+) at its growth temperature. We solved the crystal structures of tDXR with and without fosmidomycin. The structure without fosmidomycin but unexpectedly bound with 2-methyl-2,4-pentanediol (MPD), revealing a new extra space available for potential drug design. This structure adopted the closed form by rigid domain rotation but without the flexible loop over the active site, which was considered as a novel conformation. Further, the conserved Asp residue responsible for cation binding seemed to play an important role in adjusting the position of fosmidomycin. Taken together, our kinetic and the crystal structures illustrate the binding mode of fosmidomycin that leads to its slow, tight binding according to the conformational changes of DXR.

Homofarnesals: female sex attractant pheromone components of the southern cowpea weevil, Callosobruchus chinensis.

The southern cowpea weevil, Callosobruchus chinensis (Coleoptera: Bruchidae), is a major pest of stored legumes in warm temperate and tropical climates. The female sex attractant pheromone was extracted from filter-paper shelters taken from containers that housed virgin females. The extracts were purified by various chromatographic techniques, and the biologically active components in the fractions were screened by gas chromatographic-electroantennographic detection analysis with male antennae. Two compounds that elicited electrophysiological responses were isolated, and gas chromatography-mass spectrometry, nuclear magnetic resonance, and micro-chemical analyses suggested that the active compounds were homofarnesals, (2Z,6E)- and (2E,6E)-7-ethyl-3,11-dimethyl-2,6,10-dodecatrienals. Males of C. chinensis were significantly attracted to filter paper discs loaded with the synthetic compounds at 0.01-0.1 ng compared to solvent control in a Y-tube olfactometer assay. These pheromone components represent unique chemical structures within the genus Callosobruchus.

Crystallization and preliminary crystallographic analysis of hygromycin B phosphotransferase from Escherichia coli.

Aminoglycoside antibiotics, such as hygromycin, kanamycin, neomycin, spectinomycin and streptomycin, inhibit protein synthesis by acting on bacterial and eukaryotic ribosomes. Hygromycin B phosphotransferase (Hph; EC 2.7.1.119) converts hygromycin B to 7''-O-phosphohygromycin using a phosphate moiety from ATP, resulting in the loss of its cell-killing activity. The Hph protein has been crystallized for the first time using a thermostable mutant and the hanging-drop vapour-diffusion method. The crystal provided diffraction data to a resolution of 2.1 A and belongs to space group P3(2)21, with unit-cell parameters a = b = 71.0, c = 125.0 A. Crystals of complexes of Hph with hygromycin B and AMP-PNP or ADP have also been obtained in the same crystal form as that of the apoprotein.

Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase in a quaternary complex with a magnesium ion, NADPH and the antimalarial drug fosmidomycin.

The crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) from Escherichia coli complexed with Mg(2+), NADPH and fosmidomycin was solved at 2.2 A resolution. DXR is the key enzyme in the 2-C-methyl-D-erythritol 4-phosphate pathway and is an effective target of antimalarial drugs such as fosmidomycin. In the crystal structure, electron density for the flexible loop covering the active site was clearly observed, indicating the well ordered conformation of DXR upon substrate binding. On the other hand, no electron density was observed for the nicotinamide-ribose portion of NADPH and the position of Asp149 anchoring Mg(2+) was shifted by NADPH in the active site.

Contact sex pheromone components of the cowpea weevil, Callosobruchus maculatus.

The cowpea weevil, Callosobruchus maculatus, is a major pest of stored pulses. Females of this species produce a contact sex pheromone that elicits copulation behavior in males. Pheromone was extracted from filter-paper shelters taken from cages that housed females. Crude ether extract stimulated copulation in male C. maculatus. Initial fractionation showed behavioral activity in acidic and neutral fractions. Furthermore, bioassay-guided fractionation and gas chromatography-mass spectroscopy (GC-MS) analysis of active fractions revealed that the active components of the acidic fraction were 2,6-dimethyloctane-1,8-dioic acid and nonanedioic acid. These components along with the hydrocarbon fraction, a mixture of C(27)-C(35) straight chain and methyl branched hydrocarbons, had a synergistic effect on the behavior of males. Glass dummies treated with an authentic pheromone blend induced copulation behavior in males. The potential roles of the contact sex pheromone of C. maculatus are discussed.

Structural basis for sequence-dependent recognition of colicin E5 tRNase by mimicking the mRNA-tRNA interaction.

Colicin E5--a tRNase toxin--specifically cleaves QUN (Q: queuosine) anticodons of the Escherichia coli tRNAs for Tyr, His, Asn and Asp. Here, we report the crystal structure of the C-terminal ribonuclease domain (CRD) of E5 complexed with a substrate analog, namely, dGpdUp, at a resolution of 1.9 A. Thisstructure is the first to reveal the substrate recognition mechanism of sequence-specific ribonucleases. E5-CRD realized the strict recognition for both the guanine and uracil bases of dGpdUp forming Watson-Crick-type hydrogen bonds and ring stacking interactions, thus mimicking the codons of mRNAs to bind to tRNA anticodons. The docking model of E5-CRD with tRNA also suggests its substrate preference for tRNA over ssRNA. In addition, the structure of E5-CRD/dGpdUp along with the mutational analysis suggests that Arg33 may play an important role in the catalytic activity, and Lys25/Lys60 may also be involved without His in E5-CRD. Finally, the comparison of the structures of E5-CRD/dGpdUp and E5-CRD/ImmE5 (an inhibitor protein) complexes suggests that the binding mode of E5-CRD and ImmE5 mimics that of mRNA and tRNA; this may represent the evolutionary pathway of these proteins from the RNA-RNA interaction through the RNA-protein interaction of tRNA/E5-CRD.

Purification, crystallization and preliminary X-ray analysis of the catalytic domain of the Escherichia coli tRNase colicin D.

The tRNase domain of colicin D, which cleaves only tRNA(Arg)s at the 3' side of their anticodon loops, has been expressed in Escherichia coli with its inhibitor protein and purified to a form free from the inhibitor using a low-pH buffer. Crystals were obtained by the hanging-drop vapour-diffusion method at 278 K from a buffer containing 100 mM Tris-HCl pH 8.5, 22% PEG MME 2000 and 1 mM nickel(II) chloride. Diffraction data to 1.05 A resolution were collected at BL41XU, SPring-8. The crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 34.7, b = 65.5, c = 96.5 A.

Purification, crystallization and preliminary X-ray analysis of a hexameric beta-glucosidase from wheat.

The wheat beta-glucosidase TaGlu1b, which is only active in a hexameric form, was tagged with 6xHis at the N-terminus, overexpressed in Escherichia coli and purified in two steps. The protein complexed with a substrate aglycone was crystallized at 293 K from a solution containing 10 mM HEPES pH 7.2, 1 M LiSO4 and 150 mM NaCl using the hanging-drop vapour-diffusion method. Diffraction data were collected to 1.7 A at the Photon Factory. The crystal belongs to space group P4(1)32, with unit-cell parameters a = b = c = 194.65 A, alpha = beta = gamma = 90 degrees. The asymmetric unit was confirmed by molecular-replacement solution to contain one monomer, giving a solvent content of 72.1%.

Relation between tRNase activity and the structure of colicin D according to X-ray crystallography.

Colicin D is a plasmid-encoded proteinaceous toxin which kills sensitive Escherichia coli. Toxicity stems from ribonuclease activity that targets exclusively four isoacceptors of tRNA(Arg) with a cleavage position between 38 and 39 of the corresponding anticodons. Since no other tRNAs with the same sequences at 38 and 39 as tRNA(Arg)s are cleaved, colicin D should be capable of recognizing some higher order structure of tRNAs. We report here two crystal structures of catalytic domains of colicin D which have different N-terminal lengths, both complexed with its cognate inhibitor protein, ImmD. A row of positive charge patches is found on the surface of the catalytic domain, suggestive of the binding site of the tRNAs. This finding, together with our refined tRNase activity experiments, indicates that the catalytic domain starting at position 595 has activity almost equivalent to that of colicin D.

Crystallographic structures of two bisphosphonate:1-deoxyxylulose-5-phosphate reductoisomerase complexes.

We have obtained the single-crystal X-ray crystallographic structures of the bisphosphonates [(1-isoquinolinylamino)methylene]-1,1-bisphosphonate and [[(5-chloro-2-pyridinyl)amino]methylene]-1,1-bisphosphonate, bound to the enzyme 1-deoxyxylulose-5-phosphate reductoisomerase (DXR, EC 1.1.1.267, also known as 2-C-methyl-d-erythritol-4-phosphate synthase), an important target for the development of antimalarial drugs. Our results indicate that both bisphosphonates bind into the fosmidomycin binding site. The aromatic groups are in a shallow hydrophobic pocket, and the phosphonate groups are involved in electrostatic interactions with Mg2+ or a cluster of carboxylic acid groups and lysine while the fosmidomycin phosphonate-binding site is occupied by a sulfate ion (as also observed in the DXR/NADP+ structure). The availability of these two new crystal structures opens up the possibility of the further development of bisphosphonates and related systems as DXR inhibitors and, potentially, as antiinfective agents.

Genomic organization and promoter characterization of the murine dopamine receptor regulating factor (DRRF) gene.

To study the transcriptional mechanisms by which expression of the dopamine receptor regulating factor (DRRF) gene is regulated, a murine genomic clone was isolated using a DRRF cDNA as probe. A 24 kb genomic fragment which comprises 13 kb upstream of the transcription initiation site was sequenced. The promoter region lacks a TATA box and CAAT box, is rich in G+C content, and has multiple putative binding sites for the transcription factor Sp1. The DRRF gene also has consensus sequences for AP1 and AP2 binding sites. The transcriptional activity of five deletion mutants of a 1.5 kb fragment was analyzed by modulating transcription of the heterologous chloramphenicol acetyltransferase (CAT) gene in the promoterless plasmid pCAT-Basic. All mutants showed significant transcriptional activity in the murine neuroblastoma cell line NB41A3, except the construct stretching from -901 to +17. These transient expression assays suggested the presence of positive regulators between -1153 and -901 and between -118 and -93 while a negative regulator was found in the region between -901 and -118. Comparison among cell types revealed strong transcriptional activity of the DRRF promoter in neuronal NB41A3 cells and moderate activity in hepatic HepG2 and renal OK cells, but none in skeletal muscle C2C12 or glial C6 cells. These findings confirm the tissue-specific activity of the DRRF promoter and suggest that this gene shares structural and functional similarities with the dopamine receptor genes that it regulates.

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase complexed with cofactors: implications of a flexible loop movement upon substrate binding.

The key enzyme in the nonmevalonate pathway, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), has been shown to be an effective target of antimalarial drugs. Here we report the crystal structure of DXR complexed with NADPH and a sulfate ion from Escherichia coli at 2.2 A resolution. The structure showed the presence of an extra domain, which is absent from other NADPH-dependent oxidoreductases, in addition to the conformation of catalytic residues and the substrate binding site. A flexible loop covering the substrate binding site plays an important role in the enzymatic reaction and the determination of substrate specificity.