Cyanobacteria (blue-green algae) are photosynthesizing organisms that can be used as a model for analyzing light-responsive gene expression. The regulatory system of the light-responsive psbA gene with cis-elements and trans-acting factors was studied at both transcriptional and post-transcriptional levels. Positive regulation comprises DNA curvatures (CIT and RIB), upstream elements (UPE and promoter), and a light-induced sigma factor (SigD) of RNA polymerase in transcription. On the other hand, negative regulation involves mRNA instability through an AU-box under darkness. This two-step process is a candidate for a novel mechanism regulating light-responsive gene expression.
Bioprocesses, which involve biocatalysts for the production of useful compounds, are expected to become a leading player in green chemistry. The first step in bioprocess development is screening for useful biological reactions in the immense number of microorganisms with infinite diversity and versatility. This review introduces some examples of bioprocess development that started from process design stemming from the discovery of unique metabolic processes, reactions, and enzymes in microbial nucleic acid and lipid metabolisms.
The plant hormone, gibberellin (GA), regulates plant growth and development. It was first isolated as a superelongation-promoting diterpenoid from the fungus, Gibberella fujikuroi. G. fujikuroi uses different GA biosynthetic intermediates from those in plants to produce GA3. Another class of GA-producing fungus, Phaeosphaeria sp. L487, synthesizes GA1 by using the same intermediates as those in plants. A molecular analysis of GA biosynthesis in Phaeosphaeria sp. has revealed that diterpene cyclase and cytochrome P450 monooxygenases were involved in the plant-like biosynthesis of GA1. Fungal ent-kaurene synthase is a bifunctional cyclase. Subsequent oxidation steps are catalyzed by P450s, leading to biologically active GA1. GA biosynthesis in plants is divided into three steps involving soluble enzymes and membrane-bound cytochrome P450. The activation of plant GAs is catalyzed by soluble 2-oxoglutarate-dependent dioxygenases, which is in contrast to the catalysis of fungal GA biosynthesis. This difference suggests that the origin of fungal GA biosynthesis is evolutionally independent of that in plants.
A novel FAD-dependent glucose dehydrogenase (FAD-GDH) was found and its enzymatic property for glucose sensing was characterized. FAD-GDH oxidized glucose in the presence of some artificial electron acceptors, except for O2, and exhibited thermostability, high substrate specificity and a large Michaelis constant for glucose. FAD-GDH was applied to an amperometric glucose sensor with Fe(CN)63− as a soluble mediator. The use of a relatively high concentration of Fe(CN)63− resulted in a good linearity between the current response and the glucose concentration, taking into account a large Michaelis constant for Fe(CN)63−. The glucose sensor was completely insensitive to O2 and responded linearly to glucose up to 30 mM. Compared to glucose, the response to other saccharides was negligible. The sensor can be stored at room temperature in a desiccator for at least one month without any change in the response or activity.
The biosynthetic gene cluster for the polyene antifungal antibiotic, 2′-O-methylmyxalamide D, was cloned from myxobacterium Cystobacter fuscus AJ-13278. A sequence analysis of the 12.8-kb region in the gene cluster revealed the presence of two type I polyketide synthase genes, mmxB and mmxC. The involvement of these two genes in the biosynthesis of 2′-O-methylmyxalamide D was confirmed by a gene disruption experiments. In addition, an S-adenosylmethionine-dependent methyltransferase gene (mmxM) was found downstream of the gene cluster and demonstrated, by a gene disruption analysis, to be responsible for converting the known unmethylated precursor, myxalamide D, into 2′-O-methylmyxalamide D.
Two prostaglandins, PGA2 and PGB2, were isolated from the Okinawan zoanthid, Palythoa kochii, during a search for paclitaxel-like neurite-degenerating compounds from natural sources using a cell-based assay method. In the presence of PGA2 at 30 μM, the neuronal processes induced in PC12 cells by the nerve growth factor (NGF) degenerated over 24 h, whereas PGB2 had no effect on the neuronal processes of PC12 cells. This activity of PGA2 was similar to that of the microtubule-stabilizing agents, paclitaxel (Taxol®) and epothilone A, unlike the microtubule-depolymerizing agent, colchicine, which brought about quick neurite degeneration within 3 h. PGA2 stimulated tubulin polymerization, although less potently than paclitaxel. An examination of structure-activity relationships across several PGs suggests that the cyclopentenone ring structure and the orientation of its dipolar moment played an important role in the paclitaxel-like neurite-degenerating activity. These results suggest that the cyclopentenone-type PGs can interact with microtubules to inhibit their function like paclitaxel.
A glandular secretion of the civet cat, (2S,6S)-(6-methyltetrahydropyran-2-yl)acetic acid 1 and its enantiomer, were synthesized from the yeast-reduction product and recovered substrate from yeast reduction.
Two new taxanes with a dimethylamino group on the C-5 side chain were identified for the first time in the needles of the Canadian yew, Taxus canadensis. Their structures were characterized as 7β,10β,13α-triacetoxy-5α-(3′-dimethylamino-3′-phenylpropanoyl)oxy-2α-hydroxy-2(3→20)abeotaxa-4(20),11-dien-9-one (1) and 2α,10β-diacetoxy-9α-hydroxy-5α-(3′-dimethylamino-3′-phenylpropanoyl)oxy-3,11-cyclotax-4(20)-en-13-one (2).
A series of ethyl 4-(2-aryloxyhexyloxy)benzoates was prepared and tested for their activity to induce precocious metamorphosis in larvae of the silkworm. Phenyl analog 5 showed activity comparable to that of the 6-methyl-3-pyridyl analog reported as a novel anti-JH agent. The activity of 5 could be fully counteracted by methoprene, a JH agonist. The ethoxycarbonyl group of 5 was essential for its activity.
In order to investigate the control mechanism of flavonol biosynthesis of grapevine, we obtained five genomic sequences (FLS1 to FLS5) of putative flavonol synthase genes from Vitis vinifera cv. Cabernet Sauvignon. The mRNA of five FLSs accumulated in flower buds and flowers, while the mRNA of FLS2, FLS4, and FLS5 accumulated in small berry skins and then decreased toward veraison. At the ripening stage, the mRNA of only FLS4 and FLS5 accumulated again. This change in mRNA accumulation did not contradict the flavonol accumulation in the berry skins. Shading of the berries completely inhibited the increase in flavonol content and mRNA accumulation of FLS4, but did not affect the mRNA accumulation of FLS5. The effects of light and plant hormones on flavonol accumulation were different from those on anthocyanin accumulation. Thus flavonol biosynthesis appears to be under a different control system from that of anthocyanin biosynthesis.
The most chilling-sensitive stage of rice has been found to be at the onset of microspore release. The microsporocytes produce a wall of callose between the primary cell wall and the plasma membrane, and it has been shown that precise regulation of callose synthesis and degradation in anther is essential for fertile pollen formation. In this study, genes for 10 callose synthases in the rice genome were fully annotated and phylogenetically analyzed. Expression analysis of these genes showed that OsGSL5, an ortholog of microsporogenesis-related AtGSL2, was specifically expressed in anthers, and was notably downregulated by cooling treatment. Gene expression profiles of Rho-type small GTP-binding proteins in rice anther were also analyzed. The mechanisms of callose synthesis in rice pollen formation and its relationships with cool tolerance are discussed.
Genes involved in lipid accumulation were identified in Saccharomyces cerevisiae using transposon insertion mutagenesis. Five ORFs, such as SNF2, IRA2, PRE9, PHO90, and SPT21 were found from the analysis of the insertion sites in transposon insertion mutants with higher lipid content. Since these ORFs are not directly involved in storage lipid biosynthesis, we speculate that they are involved in carbon fluxes into storage lipids in response to nutrient conditions. Lipid analysis of disruptants of these ORFs indicated that the Δsnf2, and Δira2 disruptants had significantly higher lipid content. Cultivation in a nitrogen-limited medium increased the lipid content in all disruptants, among which the Δpre9 disruptant was the most sensitive to nitrogen limitation. We then focused on the Δsnf2 disruptant due to its higher lipid content and its function as a regulator of phospholipid synthesis. Lipid class analysis indicated that triacylglycerol and free fatty acids contributed to the increase in total lipids of the Δsnf2 disruptant. The addition of exogenous fatty acids was not so effective at increasing the lipid content in the Δsnf2 disruptant as it was in the wild type. It should be noticed that exogenous free linoleic acid was much higher in the Δsnf2 disruptant than in the wild type, as in the case of endogenous free fatty acids. In addition, the incorporation of exogenous fatty acids into cells increased in the disruptant, suggesting that fatty acid transporters were regulated by SNF2. The results suggest that metabolic fluxes into storage lipids, which are activated in the Δsnf2 disruptant, is repressed by the incorporation of exogenous fatty acids. They provide new insight into the biosynthesis of storage lipids in yeast.
Clostridium stercorarium F-9 pectate lyase Pel9A is a modular enzyme composed of two hypothetical family-9 catalytic modules of the polysaccharide lyases, CM9-1 and CM9-2, in order from the N terminus. In this study, we constructed and characterized CM9-1 and CM9-2 polypeptides as rCM9-1 and rCM9-2 respectively. Both of them, like the full-length Pel9A, required the Ca2+ ion for their enzyme activities and showed high activity toward polygalacturonic acid but lower activity toward pectin. The specific activity of rCM9-2 was three times higher than that of rCM9-1 and rCM9-2 by itself efficiently catalyzed the depolymerization reaction of polygalacturonic acid into monosaccharide as the major product. It was found that rCM9-1 and rCM9-2 adsorbed to polygalacturonic acid and pectin on native affinity PAGE analysis, suggesting that they contain an independent carbohydrate-binding module separable from a catalytic module or consist of a catalytic module with a binding affinity for pectic substrates.
p-Nitrophenyl and eugenyl β-primeveroside (6-O-β-D-xylopyranosyl-β-D-glucopyranoside) hydrolytic activity was found in culture filtrate from Penicillium multicolor IAM7153, and the enzyme was isolated. The enzyme was purified as a β-primeverosidase-like enzyme by precipitation with ammonium sulfate followed by successive chromatographies on Phenyl Sepharose, Mono Q, and β-galactosylamidine affinity columns. The molecular mass was estimated to be 50 kDa by SDS–PAGE and gel filtration. The purified enzyme was highly specific toward the substrate p-nitrophenyl β-primeveroside, which was cleaved in an endo-manner into primeverose and p-nitrophenol, but a series of β-primeveroside as aroma precursors were hydrolyzed only slightly as substrates for the enzyme. In analyses of its hydrolytic action and kinetics, the enzyme showed narrow substrate specificity with respect to the aglycon and glycon moieties of the diglycoside. We conclude that the present enzyme is a kind of β-diglycosidase rather than β-primeverosidase.
In this study, 10 troponin T isoforms from adult porcine skeletal muscle messenger RNA were clarified. These were eight fast- and two slow-type isoforms. Fast-type isoforms had three and two variable exons in the N-terminal and the C-terminal region respectively. Slow-type isoforms had one variable exon in the N-terminal region.
Two squash family protease inhibitors were obtained from wax gourd (Benicasa hispida [Thunb] Cogn.). Even though they were distinctly separated by reversed-phase chromatography, the amino acid sequences of two inhibitors were identical. Both inhibitors were converted into each other, perhaps due to cis-trans isomerization of characteristic Pro in the C-terminal region.
We often eat heat-coagulated (H-C) food proteins, but there have been few studies on the allergenic activity of H-C proteins after digestion and absorption in vivo. To show that H-C protein is not an allergen after digestion, mice were used to investigate the digestion and absorption of the protein through the intestinal epithelium into portal blood employing immunoblotting and competitive inhibition ELISA. Ovalbumin (OVA) was used as the model protein, and H-C OVA was prepared by heating a 5% OVA solution for 15 min in boiling water. Antigenic OVA was not detected in the soluble fraction of gastrointestinal contents or the portal blood of mice administered H-C OVA. Also, voluntary physical activities, as an assessment of anaphylaxis, were monitored for 15 h using OVA sensitized mice. Compared to the voluntary physical activities of sensitized mice without any load, no decrease in activity was observed in the group administered H-C OVA, but a significant decrease in activity was found in the mice administered unheated OVA. These results strongly indicate that H-C OVA does not retain allergenic properties.
Nonenzymatic glycation between ovalbumin (OVA) and seven D-aldohexoses was carried out to study the chemical and antioxidant characteristics of sugar–protein complexes formed in the dry state at 55 °C and 65% relative humidity for 2 d through the Maillard reaction (MR). The effects of Maillard reaction products (MRPs) modified with different aldohexoses on radical scavenging, lipid oxidation, and tetrazolium salt (XTT) reducibility were investigated. The results showed that the degree of browning and aggregation and the tryptophan-related fluorescent intensity of glycated proteins displayed a noticeable difference that depended on the sugars used for modification. All the glycated proteins exhibited higher antioxidant activity as compared to a heated control and native OVA, and the antioxidant activity was well correlated with browning development. Furthermore, the order of antioxidant activities for the seven complexes was as follows: altrose/allose–OVAs > talose/galactose–OVAs > gulose–OVA > mannose/glucose–OVAs. This implies that sugar–protein complexes with two sugars known as epimers about C-2 showed a similar antioxidant capacity. From these results, the configuration of a hydroxyl (OH) group about position C-2 did not influence the advanced cross-linking reaction, but the configuration of OH groups about C-3 and C-4 might be very important for formation of MRPs and their antioxidant behaviors.
Butyrate induces apoptosis of various cancer cell lines in a p53-independent manner and inhibits the proliferation of cancer cells. In a previous report, we reported a significant reduction in tumor incidence in rat colon as a result of dietary sodium gluconate (GNA). The stimulation of apoptosis through enhanced butyrate production in the large intestine was involved in the antitumorigenic effect of GNA. In the present study, a cDNA microarray analysis was performed to investigate the particular mechanism involved in the antitumorigenic effect of GNA. Some up-regulated genes suggested by microarray analysis were further evaluated using real-time PCR. A microarray revealed that GNA regulates the expression of retinoic acid receptor (RAR) and retinoid X receptor (RXR), and several genes known as the target of retinoids in cancer cells. In other words, the antitumorigenic effect of GNA may involve the regulation of the retinoid signaling pathway by butyrate in a retinoid-independent manner.
The effects of sugars (xylose, arabinose, fucose, fructose, galactose, glucose, sorbitol, maltose, sucrose, and lactose; 0–20% w/v) on the properties of the pressure-induced gel from a whey protein isolate (20%, 800 MPa, 30 °C, 10 min) were studied. All the sugars decreased the hardness, breaking stress and water-holding capacity of the gel at the same concentration of 55.5 mM. Increasing the sugar content changed the microstructure of the gel from a honeycomb-like structure to a stranded structure, while the strand thickness was progressively reduced. These results suggest that sugars decreased the degree of intermolecular S–S bonding of proteins and non-covalent interaction, and restrained the phase separation during gelation under high pressure.
A practical method for universal evaluation of the astringency of green tea infusion by a taste sensor system was established. The use of EGCg aqueous solution as a standard enabled analysis with high accuracy and reproducibility. The sensor output was converted into taste-intensity on the basis of Weber’s and Weber-Fechner laws, which was named the “EITast” value (“EIT” and “ast” are abbreviations for “Estimated Intensity of Taste” and “astringency” respectively). It was clarified that green tea infusion is to be classified into eight grades on the EITast scale. Furthermore, the high correlation of the EITast value with the human gustatory sense and the high stability of the taste sensor were proved.
Stored cut lettuce gradually turns brown on the cut section after several days of storage, because cutting induces phenylalanine ammonia-lyase (PAL) activity, the biosynthesis of polyphenol is promoted, and the polyphenols are oxidized by polyphenol oxidase. In this study, we screened for inhibitors of PAL derived from fermented broths of microbes and from foods and found that a cinnamon extract definitely inhibited PLA of cut lettuce. An active component was isolated by chromatographic procedures and was identified as trans-cinnamaldehyde. Browning of cut lettuce immersed in a solution containing trans-cinnamaldehyde was definitely repressed.
Adiponectin is thought to be an important mediator of insulin sensitivity and atherosclerosis. Using mouse 19 SMXA recombinant inbred (RI) strains, a powerful tool for analyzing multifactorial genetic traits, we found relationships between serum adiponectin levels and diabetes-related traits, body mass index, and serum lipid levels, and also determined the loci controlling serum adiponectin levels by quantitative trait loci (QTL) analysis. RI strains exhibited widely ranging serum adiponectin concentration distribution patterns and diabetes-related traits. The serum adiponectin concentration showed the strongest negative correlation with fasting serum insulin concentration, but negative correlations were also observed with serum triglycerides, cholesterol, and liver weight. In contrast, neither the body mass index nor the blood glucose concentration correlated with serum adiponectin levels. These results suggest that hypoadiponectinemia might be used as a predictor of insulin resistance. In addition, two suggestive QTLs for serum adiponectin concentration were detected on Chromosome (Chr) 7, and an A/J allele at these loci was associated with elevated serum adiponectin concentrations. Identification of genes responsible for regulating the serum adiponectin concentration might lead to the development of novel treatments for patients with diabetes concomitant with hypoadiponectinemia.
Orally administered methanol extract of Passiflora edulis rind (10 mg/kg or 50 mg/kg) or luteolin (50 mg/kg), which is one of consistent polyphenols of the extract, significantly lowered systolic blood pressure in spontaneously hypertensive rats (SHRs). Quantitative analysis by liquid chromatography tandem mass spectrometry (LC-MS/MS) showed that the extract contained 20 μg/g dry weight of luteolin and 41 μg/g dry weight of luteolin-6-C-glucoside. It also contained γ-aminobutyric acid (GABA, 2.4 mg/g dry weight by LC-MS/MS or 4.4 mg/g dry weight by amino acid analysis) which has been reported to be an antihypertensive material. Since the extract contained a relatively high concentration of GABA, the antihypertensive effect of the extract in SHRs might be due mostly to the GABA-induced antihypertensive effect and partially to the vasodilatory effect of polyphenols including luteolin.
The edible thorny oyster, Spondylus varius (Mizuiri-shoujou), was found to suppress the carbon tetrachloride-induced increase in serum aspartate and alanine aminotransferase activities in mice. Significant suppressive effects on these enzyme activities were found in the fraction eluted with 75% ethanol from polystyrene gel in a dose-dependent manner. These results suggest that S. varius exerts a protective effect against liver injury.
A comparison of the volatile profiles between Korean and Japanese Shiranui cold-pressed peel oil was performed by GC and GC–MS. Limonene was the most abundant in the Japanese (91.8%) and Korean (86.4%) oil. Alcohols accounted for 1.8% in the Korean oil, and 0.2% in the Japanese oil, in which the respective linalool levels were 1.2% and 0.1%. The level of aldehydes was also higher in the Korean oil (1.6%) than in the Japanese oil (0.7%).
Some strains of Saccharomyces cerevisiae form a biofilm called a “flor” on the surface of wine after ethanolic fermentation, but the molecular mechanism of flor formation by the wild-type flor strain involved in wine making is not clear. Previously, we found that expression of the C-terminally truncated form of NRG1 (NRG11-470) on a multicopy plasmid increases the hydrophobicity of the cell surface, conferring flor formation on the non-flor laboratory strain. Here we show that in Ar5-H12, a wild-type flor haploid strain, flor formation is regulated by NRG11-470. Moreover, the disruptant of the wild-type flor diploid strain (Δflo11/Δflo11) show a weak ability to form the flor. The expression of FLO11 is always high in the wild-type flor strain, regardless of carbon source. Thus FLO11 is primary factor for wild-type flor strains. Furthermore, the disruptant (Δflo11) shows lower hydrophobicity of cell surface than the wild type. However, the hydrophobicity of the wild-type flor strains grown in ethanol medium was much higher than those grown in glucose medium. These results indicate that cell surface hydrophobicity is closely related to flor formation in wild-type flor yeasts.
Twenty-three strains, which were assigned to Gluconobacter frateurii and maintained at Culture Collection NBRC, were re-identified at the species level on the basis of restriction analysis of 16S-23S rDNA ITS regions by digestion with six restriction endonucleases: Bsp1286I, MboII, AvaII, TaqI, BsoBI, and BstNI. The strains examined were divided into six groups, Group III-1, Group III-2, Group III-3, Group III-4, Group III-5, and Group IV. Group III-1 and Group III-4 respectively were divided into two subgroups, Subgroup III-1a, Subgroup III-1b and Subgroup III-4a, Subgroup III-4b. Gluconobacter frateurii NBRC 3264T was included in Group III-2, along with strains NBRC 3265 and NBRC 3270, and G. thailandicus BCC 14116T was included in Group III-3, along with strains NBRC 3254, NBRC 3256, NBRC 3258, NBRC 3255, and NBRC 3257. These groupings were supported by a phylogenetic tree based on 16S-23S rDNA ITS sequences. Strains of group III-2 and Group IV were unequivocally re-identified as G. frateurii, but strains of Group III-3, Group III-4, and Group III-5 were not necessarily re-identified as G. frateurii. The results obtained indicate that the 23 strains have a taxonomically heterogeneous nature, and they are referred to as the G. frateurii complex.
An agar-degrading bacterium, strain SA7, was isolated from plant roots cultivated in soil. Analysis of the 16S rDNA sequence showed that strain SA7 is affiliated with the genus Asticcacaulis. Strain SA7 produced extracellular agarase, and grew utilizing agar in the culture medium as sole carbon source. Zymogram analysis showed that strain SA7 extracellularly secreted single agarase protein (about 70 kDa).
pLS20-mediated conjugational transfer between Bacillus subtilis was investigated not on conventional solid media but in liquid culture. Detailed conjugational kinetics revealed that pLS20 transmission occurred at a limited cellular growth stage of both donor and recipient. Mutation of the recipient recA did not significantly interfere with the conjugational transfer process.
Deep-sea sediment samples were collected at a depth of 3,064 m in the Japan Sea. Microorganisms in the sediment sample were cultivated under several pressure conditions, and the high-pressure adapted microbes were isolated. Two of the isolates exhibited piezophilic growth profiles. This is the first report to show the presence of piezophiles in the Japan Sea.
Symbiobacterium thermophilum is a unique syntrophic bacterium that exhibits marked growth only in coculture with a cognate Bacillus sp. In this study, we found that the bacterium is capable of marked mono-growth when supplied with CO2 or bicarbonate. The evidence suggests that the genetic defect for carbonic anhydrase in this bacterium is a reason for the syntrophic property based on CO2 requirement.