Hiroshi Habe

National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan

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Publications (104)266.98 Total impact

  • Shun Sato, Dai Kitamoto, Hiroshi Habe
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    ABSTRACT: We demonstrate that 0.78 mm glyceric acid activated the proliferation of human dermal fibroblasts by about 45%, whereas 34 mm α-glucosylglyceric acid (GGA) increased collagen synthesis by the fibroblasts by 1.4-fold compared to that in the absence of GGA. The two substances also exerted protective effects on both DNA scission by the hydroxyl radical and protein aggregation by heat in vitro.
    Bioscience Biotechnology and Biochemistry 07/2014; 78(7):1183-1186. · 1.27 Impact Factor
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    ABSTRACT: Carbazole 1,9a-dioxygenase (CARDO), a Rieske non-heme iron oxygenase (RO), is a three-component system composed of terminal oxygenase (Oxy), ferredoxin, and ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy gene from Janthinobacterium sp. strain J3 generated the Oxy derivatives I262V, F275W, Q282N and Q282Y, which showed different oxygenation capabilities than the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. I262V, F275W, and Q282Y catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15°, 25°, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and imino nitrogen of carbazole. In the crystal structure of F275W complexed with fluorene, C9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate binding position that in turn favors specific oxygenation reactions toward various substrates.
    Applied and Environmental Microbiology 02/2014; · 3.95 Impact Factor
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    ABSTRACT: Gluconobacter oxydans IFO12528 is able to produce glyceric acid (GA) from glycerol through the action of a membrane-bound alcohol dehydrogenase (mADH), which is required for GA production. To determine whether membrane-bound aldehyde dehydrogenase (mALDH) also plays a role in GA production in G. oxydans, we constructed an aldH-disrupted mutant of G. oxydans (ΔaldH). ΔaldH was unable to produce acetic acid from ethanol, but was able to produce GA at a level approximately half that of the wildtype strain, suggesting the involvement of another ALDH in GA production. We also investigated the enantiomeric composition of GA produced by the IFO12528 and ΔaldH strains. No difference in GA composition was evident in the ΔaldH mutant, with ~73% d-GA enantiomeric excess observed in both strains.
    Journal of oleo science 01/2014; 63(9):953-7. · 1.24 Impact Factor
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    ABSTRACT: The basidiomycetous yeast Pseudozyma antarctica is known as a producer of industrial enzymes and the extracellular glycolipids, mannosylerythritol lipids. Here, we report the draft genome sequence of the type strain JCM10317. The draft genome assembly has a size of 18.1 Mb and a G+C content of 60.9%, and it consists of 197 scaffolds.
    Genome announcements. 01/2014; 2(5).
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    ABSTRACT: Pseudozyma antarctica is a non-pathogenic phyllosphere yeast known as an excellent producer of mannosylerythritol lipids (MELs), multi-functional extracellular glycolipids, from vegetable oils. To clarify the genetic characteristics of P. antarctica, we analyzed the 18 Mb genome of P. antarctica T-34. On the basis of KOG analysis, the number of genes (219 genes) categorized into lipid transport and metabolism classification in P. antarctica was one and a half times larger than that of yeast Saccharomyces cerevisiae (140 genes). The gene encoding an ATP/citrate lyase (ACL) related to acetyl-CoA synthesis conserved in oleaginous strains was found in P. antarctica genome: the single ACL gene possesses the four domains identical to that of the human gene, whereas the other oleaginous ascomycetous species have the two genes covering the four domains. P. antarctica genome exhibited a remarkable degree of synteny to U. maydis genome, however, the comparison of the gene expression profiles under the culture on the two carbon sources, glucose and soybean oil, by the DNA microarray method revealed that transcriptomes between the two species were significantly different. In P. antarctica, expression of the gene sets relating fatty acid metabolism were markedly up-regulated under the oily conditions compared with glucose. Additionally, MEL biosynthesis cluster of P. antarctica was highly expressed regardless of the carbon source as compared to U. maydis. These results strongly indicate that P. antarctica has an oleaginous nature which is relevant to its non-pathogenic and MEL-overproducing characteristics. The analysis and dataset contribute to stimulate the development of improved strains with customized properties for high yield production of functional bio-based materials.
    PLoS ONE 01/2014; 9(2):e86490. · 3.53 Impact Factor
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    ABSTRACT: To promote the effective use of raw glycerol, 13 yeast strains with the ability to produce mannitol from glycerol were isolated from environmental samples. Of the 13 strains, strain 7-12G was selected as an efficient mannitol producer from 25% (w/v) glycerol and was identified as Candida azyma by morphological, physicochemical, and phylogenetic analyses. When the ability to produce mannitol from raw glycerol in flask culture was compared among strains 7-12G, NBRC10406 (the type strain of C. azyma), and related strains, strain NBRC10406 exhibited the highest production level (31.8 g/l). Culture in jar fermentors was next investigated, and mannitol production reached 50.8 g/l over 7 days, corresponding to 0.30 g/g-glycerol. To the best of our knowledge, this is the highest reported level of mannitol produced by a microbe from glycerol under batch-type culture conditions.
    Journal of Bioscience and Bioengineering 12/2013; · 1.74 Impact Factor
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    ABSTRACT: To promote the effective use of raw glycerol (a by-product of biodiesel production), 110 yeast strains that produce D-arabitol from glycerol were isolated from environmental samples. Among them, strain 17-2A was an effective D-arabitol producer in the presence of 250 g/l glycerol and was identified as Candida quercitrusa based on morphological, physicochemical, and phylogenetic analyses. C. quercitrusa type strain NBRC1022 produced the greatest quantity of D-arabitol (41.7 g/l) when the ability to produce D-arabitol from raw glycerol was compared among C. quercitrusa 17-2A and its phylogenetically related strains in flask culture. Under optimized culture conditions, strain NBRC1022 produced D-arabitol at a concentration of 58.2 g/l after a 7-day cultivation in 250 g/l glycerol, 6 g/l yeast extract, and 2 g/l CaCl2. The culture conditions were further investigated with raw glycerol using a jar fermenter; the concentration of D-arabitol reached 67.1 g/l after 7 days and 85.1 g/l after 10 days, respectively, which corresponded to 0.40 g/g of glycerol. To our knowledge, the present D-arabitol yield from glycerol is higher than reported previously using microbial production.
    Applied Microbiology and Biotechnology 12/2013; · 3.69 Impact Factor
  • Shun Sato, Dai Kitamoto, Hiroshi Habe
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    ABSTRACT: To produce glyceric acid (GA) from methanol-containing glycerol, resistance to methanol of Gluconobacter frateurii NBRC103465 was improved by chemical mutagenesis using N-methyl-N'-nitro-N-nitrosoguanidine. The obtained mutant Gf398 produced 6.3 g/L GA in 5% (v/v) methanol-containing 17% (w/v) glycerol medium, in which the wild-type strain neither grew nor produced GA.
    Journal of Bioscience and Bioengineering 08/2013; · 1.74 Impact Factor
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    ABSTRACT: To enhance the value-added use of methanol-containing raw glycerol derived from biodiesel fuel production, the effect of methanol supplementation on glyceric acid (GA) production by Gluconobacter spp. was investigated. We first conducted fed-batch fermentation with Gluconobacter frateurii NBRC103465 using raw glycerol as a feeding solution. GA productivity decreased with increasing dihydroxyacetone (DHA) formation when the raw glycerol contained methanol. The results of this experiment and comparative experiments using a synthetic solution modeled after the raw glycerol indicate that the presence of methanol caused a change in the concentrations of GA and DHA, two glycerol derivatives produced during fermentation. Other Gluconobacter spp. also decreased GA production in the presence of 1% (v/v) methanol. In addition, purified membrane-bound alcohol dehydrogenase (mADH) from Gluconobacter oxydans, which is a key enzyme in GA production, showed a decrease in dehydrogenase activity toward glycerol as the methanol concentration increased. These results strongly suggest that the observed decrease in GA production by Gluconobacter spp. resulted from the methanol-induced inhibition of mADH-mediated glycerol oxidation.
    AMB Express. 04/2013; 3(1):20.
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    ABSTRACT: Gluconobacter frateurii strain NBRC 103465 can efficiently produce glyceric acid (GA) from raw glycerol feedstock derived from biodiesel fuel production processes. Here, we report the 3.4-Mb draft genome sequence of G. frateurii NBRC 103465. The draft genome sequence can be applied to examine the enzymes and electron transport system involved in GA production.
    Genome announcements. 01/2013; 1(4).
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    ABSTRACT: Some acetic acid bacteria have been shown to produce large amounts of glyceric acid (GA) from glycerol, which is a by-product of biodiesel fuel (BDF) production. Previously, a Gluconobacter strain was found that produced decreased amounts of GA from glycerol in the presence of methanol, a major ingredient of raw glycerol derived from the BDF industry. Thus, a comparative transcriptome analysis of Gluconobacter frateurii NBRC103465 was performed to investigate changes in gene expression during GA production from glycerol in the presence of methanol. Cells grown with methanol showed upregulated expression of a class III alcohol dehydrogenase homolog (adhCGf) and decreased GA production. adhCGf was cloned and expressed heterologously in Escherichia coli, and the presence of an additional protein with an approximate molecular mass of 39 kDa in the cytosol of the recombinant E. coli cells was identified by SDS-PAGE. Activity measurements of the cytosol revealed that the translational product of adhCGf exhibited formaldehyde dehydrogenase activity in the presence of nicotinamide adenine dinucleotide and glutathione. Gluconobacter frateurii cells grown in 1% methanol-containing glycerol were found to have fivefold higher formaldehyde dehydrogenase activity than cells grown without methanol, suggesting that adhCGf in G. frateurii cells functions in the dissimilation of methanol-derived formaldehyde.
    Journal of oleo science 01/2013; 62(10):835-842. · 1.24 Impact Factor
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    ABSTRACT: A dibenzofuran (DF)-degrader Terrabacter sp. strain DBF63 harbors the dbfA and dbfBC genes for DF degradation and the fln-dbfA, pht, and pca gene clusters for the utilization of fluorene (FN) as a sole carbon source. From this strain, dfdA1, the gene encoding the second DF dioxygenase was detected using degenerate polymerase chain reaction (PCR) and the dfdA1A2A3A4 genes were cloned from a cosmid library of the DBF63 genome. Nucleotide sequencing revealed that the dfdA genes showed considerably high identities with those of other actinobacteria, such as Terrabacter sp. strain YK3 and Rhodococcus sp. strain HA01. In the neighboring region of the dfdA genes, as many as 11 homologs for transposase and integrase genes and the putative extradiol dioxygenase gene disrupted by an insertion sequence (dfdB::ISTesp2) were found, suggesting that repeated gene rearrangement had occurred. Quantitative reverse transcription-PCR analysis revealed that dfdA1 was expressed primarily in the DF-fed strain, whereas dbfA1 was expressed in the FN-cultured strain, apparently indicating that the dfdA genes are induced by DF for the initial hydroxylation of DF in strain DBF63. Furthermore, two polycistronic gene cassettes consisting of either dfdA or dbfA together with the dbfBC gene were constructed and expressed heterologously in Streptomyces lividans, degrading DF to salicylate. Furthermore, the expressed DfdA dioxygenase degraded dibenzo-p-dioxin, carbazole, dibenzothiophene, anthracene, phenanthrene, and biphenyl, thereby exhibiting a broader substrate range than that of the DbfA dioxygenase.
    Applied Microbiology and Biotechnology 11/2012; · 3.69 Impact Factor
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    ABSTRACT: Glyceric acid (GA) is one of the most promising functional hydroxyl acids, and it is abundantly obtained from glycerol by a bioprocess using acetic acid bacteria. In this study, several monoacyl GAs were synthesized by esterification of GA and saturated fatty acyl chlorides (C12, C14, C16, and C18), forming a new class of bio-based surfactants. By the present method, a mixture of two isomers, namely 2-O-acyl and 3-O-acyl GAs, was produced, in which the 2-O-acyl derivatives were obtained as a major product. These isomers were isolated, and their surface-active properties were investigated for the first time. The surface tensions of 2-O-acyl GAs with different chain lengths were determined by the Wilhelmy method. At concentrations below 10(-4) M, the 2-O-acyl GAs exhibited higher surface-active properties compared to commercially available synthetic surfactants. For example, 2-O-lauroyl GA reduced the surface tension of water to around 25 mN/m above the critical micelle concentration (3.0×10(-4) M). In addition, 2-O-acyl derivatives showed higher surface-tension-lowering activity than 3-O-acyl GAs. The monoacyl GAs synthesized herein can potentially be used as "green surfactants."
    Journal of oleo science 01/2012; 61(6):343-8. · 1.24 Impact Factor
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    ABSTRACT: 2,3-O-Dipalmitoyl-D-glyceric acid (PA2-DGA) was synthesized from D-glyceric acid calcium salt and palmitoyl chloride with improved yield. Direct condensation between the D-glyceric acid calcium salt and palmitoyl chloride produced PA2-DGA with a yield of <10%, whereas stepwise synthesis yielded this compound at up to 24% of overall yield. PA2-DGA was then subjected to a cytotoxic test using normal human dermal fibroblasts and primary normal human dermal microvascular endothelial cells. This compound had no toxic effects on human cells in vitro at concentrations up to 34 µM.
    Journal of oleo science 01/2012; 61(6):337-41. · 1.24 Impact Factor
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    ABSTRACT: Utilization of excess glycerol supplies derived from the burgeoning biodiesel industry has recently become very important. Glyceric acid (GA) is one of the most promising glycerol derivatives, and it is abundantly obtained from glycerol by a bioprocess using acetic acid bacteria. In this study, a novel branched-type poly(lactic acid) (PLA) was synthesized by polycondensation of lactide in the presence of GA. The resulting branched PLA had lower crystallinity and glass transition temperatures than the conventional linear PLA, and the peak associated with the melting point of the branched PLA disappeared. Moreover, in a blend of the branched polymer, the crystallization of the linear PLA occurred at a lower temperature. Thus, the branched PLA containing GA synthesized in this study could potentially be used as a novel bio-based modifier for PLA.
    Journal of oleo science 01/2011; 60(7):369-73. · 1.24 Impact Factor
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    ABSTRACT: D-Glyceric acid (D-GA) calcium has been reported to accelerate ethanol oxidation in vivo in rats (Eriksson et al., Metabolism, 56, 895-898 (2007)). However, no other reports have shown that D-GA can reduce the harmful effects of ethanol. In this study, the effects of D-, L-, and DL-GA calcium on ethanol-dosed gastric cell viability were investigated using human gastric carcinoma cells (Kato III) and normal rat gastric mucosa cells (RGM1). Addition of 2% and 3 % ethanol to Kato III and RGM1 cells, respectively, decreased their cell viability by approximately 20-50 % after 24 or 72 h of cultivation. In 2 % ethanol-dosed Kato III cells cultivated for 24 h, addition of 0.002-20 µg/mL D- and L-GA calcium did not affect cell viability. Similarly, addition of less than 20 µg/mL DL-GA calcium did not affect cell viability. However, when 20 µg/mL DL-GA calcium was added, cell viability increased by 35.7 % after 72 h of incubation, compared to the viability of control cells without ethanol or GA. Addition of 20 µg/mL DL-GA calcium to 3 % ethanol-dosed RGM1 cells cultivated for 24 or 72 h also increased cell viability up to those observed in control cells. These results suggest that a racemic mixture of GA may have the strongest effect on enhancing the viability of ethanol-exposed cells.
    Journal of oleo science 01/2011; 60(11):585-90. · 1.24 Impact Factor
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    ABSTRACT: Previously, Lešová et al. reported the isolation and identification of metabolite OR-1, showing antitrypsin activity, produced during fermentation by Penicillium funiculosum. The structure of OR-1 was a mixture of glyceric acid (GA), esterified with C(14)-C(18) fatty acids, and oleic acid (C18:1) as the most predominant fatty acid (Folia Microbiol. 46, 21-23, 2001). In this study, dioleoyl D-GA and dioleoyl L-GA were synthesized via diesterification with oleoyl chloride, and their antitrypsin activities were evaluated using both a disk diffusion method and spectral absorption measurements. The results show that both compounds and their equivalent mixtures possess antitrypsin activities; however, their IC(50) values (approximately 2 mM) are much higher than that of OR-1 (4.25 µM), suggesting that dioleoyl GA does not play a major role in the OR-1 antitrypsin activity.
    Journal of oleo science 01/2011; 60(6):327-31. · 1.24 Impact Factor
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    ABSTRACT: A novel derivative of glyceric acid (GA), dilinoleoyl-D-glyceric acid (LA₂-DGA), was synthesized from D-GA calcium salt and linoleoyl chloride and evaluated for cytotoxicity. The D-GA calcium salt was first reacted with 4-methoxybezylchloride, and the resulting compound was esterified with linoleoyl chloride. This reaction was followed by hydrolysis of the 4-methoxybenzyl moiety, yielding LA₂-DGA. LA₂-DGA was then subjected to cytotoxicity testing using normal human dermal fibroblasts and primary normal human dermal microvascular endothelial cells. LA₂-DGA showed no significant toxic effects in either type of cell.
    Journal of oleo science 01/2011; 60(9):483-7. · 1.24 Impact Factor
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    ABSTRACT: Acetobacter tropicalis NBRC16470 can produce highly enantiomerically pure D-glyceric acid (D-GA; >99 % enantiomeric excess) from glycerol. To investigate whether membrane-bound alcohol dehydrogenase (mADH) is involved in GA production in A. tropicalis, we amplified part of the gene encoding mADH subunit I (adhA) using polymerase chain reaction and constructed an adhA-disrupted mutant of A. tropicalis (ΔadhA). Because ΔadhA did not produce GA, we confirmed that mADH is essential for the conversion of glycerol to GA. We also cloned and sequenced the entire region corresponding to adhA and adhB, which encodes mADH subunit II. The sequences showed high identities (84-86 %) with the equivalent mADH subunits from other Acetobacter spp.
    Journal of oleo science 01/2011; 60(9):489-94. · 1.24 Impact Factor
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    ABSTRACT: Pervaporation is a promising method to recover bio-alcohols from fermentation broths because of its high energy-saving potential. A silicalite membrane was prepared and applied to the pervaporation separation of 1-butanol, 2-propanol, ethanol and acetone from dilute aqueous solutions. In feed solvent concentrations in the range of 0.5−5.0 wt.%, the solvent flux of ethanol, 2-propanol and acetone increased with the increase of feed concentration, whereas 1-butanol flux was not greatly influenced by the feed concentration. In contrast to other solvents, the separation factor for 1-butanol solution decreased with the increase of feed 1-butanol concentration. This is because 1-butanol concentration in the permeate did not increase along with the increase of the feed 1-butanol concentration due to adsorption saturation. The solvent flux increased with the increase of separation temperature for all the solvents. The separation factor of 1-butanol and 2-propanol increased with the increase of separation temperature in the range of 30−60°C, while the separation factor of acetone and ethanol was not greatly influenced by the separation temperature. Silicalite membrane shows higher selectivity toward 1-butanol solutions than silicone membrane when the feed concentration is low and the temperature is high.
    Desalination and water treatment 01/2011; 34:290-294. · 0.85 Impact Factor

Publication Stats

2k Citations
266.98 Total Impact Points

Institutions

  • 2007–2014
    • National Institute of Advanced Industrial Science and Technology
      • Research Institute for Innovation in Sustainable Chemistry
      Tsukuba, Ibaraki, Japan
  • 2009
    • Tokyo University of Science
      Edo, Tōkyō, Japan
  • 1996–2009
    • The University of Tokyo
      • Center for Biotechnology Research
      Tokyo, Tokyo-to, Japan
  • 2006
    • Tohoku University
      • Department of Environmental Life Sciences
      Sendai, Kagoshima, Japan
    • Shibaura Institute of Technology
      Tōkyō, Japan
  • 2001
    • Akita Prefectural University
      • Faculty of Bioresource Sciences
      Tokyo, Tokyo-to, Japan