Hideaki Yukawa

Research Institute of Innovative Technology for the Earth, Kioto, Kyōto, Japan

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Publications (216)602.48 Total impact

  • Akira Watanabe · Kazumi Hiraga · Masako Suda · Hideaki Yukawa · Masayuki Inui ·
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    ABSTRACT: The Corynebacterium alkanolyticum xylEFGD gene cluster comprises xylD gene that encodes an intracellular β-xylosidase next to xylEFG operon encoding a substrate binding protein and two membrane permease proteins of a xyloside ABC transporter. Cloning of the cluster revealed a recombinant β-xylosidase of moderately high activity (turnover for p-nitrophenyl-β-d-xylopyranoside = 111 ± 4 s(-1)), weak α-l-arabinofuranosidase activity (turnover for p-nitrophenyl-α- l-arabinofuranoside = 5 ± 1 s(-1)) and high tolerance to product inhibition (Ki for xylose = 67.6 ± 2.6 mM). Heterologous expression of the entire cluster under the control of the strong constitutive tac promoter in Corynebacterium glutamicum xylose fermenting strain X1 enabled the resultant strain X1EFGD to rapidly utilize not only xylooligosaccharides but also arabino-xylooligosaccharides. The ability to utilize arabino-xylooligosaccharides depended on cgR_2369, a gene encoding a multitask ATP binding protein. Heterologous expression of contiguous xylD gene in strain X1 led to strain X1D with 10-fold greater β-xylosidase activity than strain X1EFGD, albeit with total loss of arabino-xylooligosaccharides utilization ability and only half the ability to utilize xylooligosaccharides. The findings suggest some inherent ability of C. glutamicum to uptake xylooligosaccharides, an ability that is enhanced by in the presence of a functional xylEFG-encoded xyloside ABC transporter. The finding that xylEFG imparts non-native ability to uptake arabino-xylooligosaccharides should be useful in constructing industrial strains with efficient fermentation of arabinoxylan, a major component of lignocellulosic biomass hydrolysates. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Applied and Environmental Microbiology 04/2015; 81(12). DOI:10.1128/AEM.00792-15 · 3.67 Impact Factor
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    ABSTRACT: We previously reported on the impacts of the overexpression of individual genes of the glycolytic pathway encoding glucokinase (GLK), glyceraldehyde phosphate dehydrogenase (GAPDH), phosphofructokinase (PFK), triosephosphate isomerase (TPI), and bisphosphate aldolase (FBA) on D-lactate productivity in Corynebacterium glutamicum under oxygen-deprived conditions. Searching for synergies, in the current study, we simultaneously overexpressed the five glycolytic genes in a stepwise fashion to evaluate the effect of the cumulative overexpression of glycolytic genes on D-lactate production. Interestingly, the final D-lactate concentration markedly differed depending on whether or not the PFK encoding gene was overexpressed when combined with overexpressing other glycolytic genes. The simultaneous overexpression of the GLK, GAPDH, TPI, and FBA encoding genes led to the highest initial D-lactate concentration at 10 h. However, this particular recombinant strain dramatically slowed producing D-lactate when a concentration of 1300 mM was reached, typically after 32 h. In contrast, the strain overexpressing the PFK encoding gene together with the GLK, GAPDH, TPI, and FBA encoding genes showed 12.7 % lower initial D-lactate concentration at 10 h than that observed with the strain overexpressing the genes coding for GLK, GAPDH, TPI, and FBA. However, this recombinant strain continued to produce D-lactate after 32 h, reaching 2169 mM after a mineral salts medium bioprocess incubation period of 80 h. These results suggest that overexpression of the PFK encoding gene is essential for achieving high production of D-lactate. Our findings provide interesting options to explore for using C. glutamicum for cost-efficient production of D-lactate at the industrial scale.
    Applied Microbiology and Biotechnology 03/2015; 99(11). DOI:10.1007/s00253-015-6546-9 · 3.34 Impact Factor
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    ABSTRACT: Rapid sugar consumption is important for the microbial production of chemicals and fuels. Here, we show that overexpression of the NADH dehydrogenase gene (ndh) increased glucose consumption rate in Corynebacterium glutamicum under oxygen-deprived conditions through investigating the relationship between the glucose consumption rate and intracellular NADH/NAD(+) ratio in various mutant strains. The NADH/NAD(+) ratio was strongly repressed under oxygen deprivation when glucose consumption was accelerated by the addition of pyruvate or sodium hydrogen carbonate. Overexpression of the ndh gene in the wild-type strain under oxygen deprivation decreased the NADH/NAD(+) ratio from 0.32 to 0.13, whereas the glucose consumption rate increased by 27 %. Similarly, in phosphoenolpyruvate carboxylase gene (ppc)- or malate dehydrogenase gene (mdh)-deficient strains, overexpression of the ndh gene decreased the NADH/NAD(+) ratio from 1.66 to 0.37 and 2.20 to 0.57, respectively, whereas the glucose consumption rate increased by 57 and 330 %, respectively. However, in a lactate dehydrogenase gene (L-ldhA)-deficient strain, although the NADH/NAD(+) ratio decreased from 5.62 to 1.13, the glucose consumption rate was not markedly altered. In a tailored D-lactate-producing strain, which lacked ppc and L-ldhA genes, but expressed D-ldhA from Lactobacillus delbrueckii, overexpression of the ndh gene decreased the NADH/NAD(+) ratio from 1.77 to 0.56, and increased the glucose consumption rate by 50 %. Overall, the glucose consumption rate was found to be inversely proportional to the NADH/NAD(+) ratio in C. glutamicum cultured under oxygen deprivation. These findings could provide an option to increase the productivity of chemicals and fuels under oxygen deprivation.
    Applied Microbiology and Biotechnology 03/2015; 99(13). DOI:10.1007/s00253-015-6540-2 · 3.34 Impact Factor
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    ABSTRACT: Reinforcing microbial thermotolerance is a strategy to enable fermentation with flexible temperature settings and thereby to save cooling costs. Here, we report on adaptive laboratory evolution (ALE) of the amino acid-producing bacterium Corynebacterium glutamicum under thermal stress. After 65 days of serial passage of the transgenic strain GLY3, in which the glycolytic pathway is optimized for alanine production under oxygen deprivation, three strains adapted to supraoptimal temperatures were isolated, and all mutations they acquired were identified by whole-genome re-sequencing. Of the 21 mutations common to the three strains, one large deletion and two missense mutations were found to promote growth of the parental strain under thermal stress. Additive effects on thermotolerance were observed among these mutations, and the combination of the deletion with the missense mutation on otsA, encoding a trehalose-6-phosphate synthase, allowed the parental strain to overcome the upper limit of growth temperature. Surprisingly, the three evolved strains acquired cross-tolerance to isobutanol, which turned out to be partly attributable to the genomic deletion associated with the enhanced thermotolerance. The deletion involved loss of two transgenes pfk and pyk, encoding the glycolytic enzymes, in addition to six native genes, and elimination of these transgenes but not the native genes was shown to account for the positive effects on thermal and solvent stress tolerance, implying a link between energy-producing metabolism and bacterial stress tolerance. Overall, the present study provides evidence that ALE can be a powerful tool to refine the phenotype of C. glutamicum and investigate molecular bases of stress tolerance. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Applied and Environmental Microbiology 01/2015; 81(7). DOI:10.1128/AEM.03973-14 · 3.67 Impact Factor
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    Haruhiko Teramoto · Hideaki Yukawa · Masayuki Inui ·
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    ABSTRACT: In Corynebacterium glutamicum R, CsoR acts as a transcriptional repressor not only of the cognate copA-csoR operon but also of the copZ1-copB-cgR_0126 operon. It is predicted that copA and copB encode P-type ATPases for copper efflux and copZ1 encodes a metallochaperone. Here, a CsoR-binding motif was found upstream of another copZ-like gene, copZ2, and the in vitro binding of the CsoR protein to its promoter was confirmed. The monocistronic copZ2 transcript was upregulated by excess copper in a CsoR-dependent manner. Among the extended CsoR regulon, deletion of copA, but not of copB, copZ1, or copZ2, resulted in decreased resistance to copper, indicating a major role of the CopA copper exporter in the multilayered systems for copper homeostasis. A redundant role of copZ1 and copZ2 in copper resistance was also indicated by double deletion of these genes. The copper-dependent activation of the copA, copZ1, and copZ2 promoters was confirmed by lacZ reporter assays, consistent with the coordinated derepression of the three transcriptional units. The copZ1 promoter activity showed the highest responsiveness to copper and was also induced by excess zinc and nickel. Furthermore, zinc-inducible expression observed for the CsoR-regulated genes was independent of Zur, recently found to uniquely act as a transcriptional repressor of zinc efflux genes. These results implied complicated cross talk between homeostasis of multiple transition metals.
    Applied Microbiology and Biotechnology 01/2015; 99(8). DOI:10.1007/s00253-015-6373-z · 3.34 Impact Factor
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    ABSTRACT: Recombinant Corynebacterium glutamicum harboring genes for pyruvate decarboxylase (pdc) and alcohol dehydrogenase (adhB) can produce ethanol under oxygen deprivation. We investigated the effects of elevating the expression levels of glycolytic genes, as well as pdc and adhB, on ethanol production. Overexpression of four glycolytic genes (pgi, pfkA, gapA, and pyk) in C. glutamicum significantly increased the rate of ethanol production. Overexpression of tpi, encoding triosephosphate isomerase, further enhanced productivity. Elevated expression of pdc and adhB increased ethanol yield, but not the rate of production. Fed-batch fermentation using an optimized strain resulted in ethanol production of 119 g/L from 245 g/L glucose with a yield of 95 % of the theoretical maximum. Further metabolic engineering, including integration of the genes for xylose and arabinose metabolism, enabled consumption of glucose, xylose, and arabinose, and ethanol production (83 g/L) at a yield of 90 %. This study demonstrated that C. glutamicum has significant potential for the production of cellulosic ethanol.
    Applied Microbiology and Biotechnology 11/2014; 99(3). DOI:10.1007/s00253-014-6223-4 · 3.34 Impact Factor
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    ABSTRACT: Shikimate can be utilized as the sole source of carbon and energy of Corynebacterium glutamicum. Although biosynthesis and degradation of shikimate are well characterized in C. glutamicum, the transport of shikimate has hardly been studied. A mutant strain deficient in cgR_2523 loses the ability to grow on shikimate as well as to consume extracellular shikimate, indicating that the gene is involved in shikimate utilization (designated shiA). The hydropathy profile of the deduced amino acid sequence indicates that ShiA belongs to the metabolite/proton symporter family, which is a member of the major facilitator superfamily. Accumulation assay showed that the uptake of shikimate was hardly detected in the shiA deficient strain but was markedly enhanced in a shiA-expressing strain. These results suggested that the uptake of shikimate was mainly mediated by the shikimate transporter encoded by shiA. The shiA mRNA induction level by shikimate was significantly decreased by the disruption of cgR_2524 (designated shiR), which is located immediately upstream of shiA and encodes a LysR-type transcriptional regulator, suggesting that ShiR acts as an activator of shiA. To our knowledge, this is the first report in Gram-positive bacteria of shikimate transporter and its regulation. Copyright © 2014, the Society for General Microbiology.
    Microbiology 11/2014; 161(Pt_2). DOI:10.1099/mic.0.083733-0 · 2.56 Impact Factor
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    Koichi Toyoda · Haruhiko Teramoto · Hideaki Yukawa · Masayuki Inui ·
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    ABSTRACT: The extracytoplasmic function sigma factor σ(H) is responsible for heat and oxidative stress response in Corynebacterium glutamicum. Due to the hierarchical nature of the regulatory network, previous transcriptome analyses have not been able to discriminate between direct and indirect targets of σ(H). Here, we determined the direct genome-wide targets of σ(H) by ChIP-chip analysis using a deletion mutant of rshA, encoding an anti-σ factor of σ(H). Seventy-five σ(H)-dependent promoters, including 39 new ones, were identified. σ(H)-dependent, heat-inducible transcripts for several of the new targets, including ilvD encoding a labile Fe-S cluster enzyme dihydroxy-acid dehydratase, were detected and their 5' -ends were mapped to the σ(H)-dependent promoters identified. Interestingly, functional internal σ(H)-dependent promoters were found in operon-like gene clusters involved in the pentose phosphate pathway, riboflavin biosynthesis, and Zn uptake. Accordingly, deletion of rshA resulted in hyperproduction of riboflavin and affected expression of Zn-responsive genes possibly through intracellular Zn overload, indicating new physiological roles of σ(H). Furthermore, sigA encoding the primary σ factor was identified as a new target of σ(H). Reporter assays demonstrated that the σ(H)-dependent promoter upstream of sigA was highly heat-inducible but much weaker than the known σ(A)-dependent one. Our ChIP-chip analysis also detected the σ(H)-dependent promoters upstream of rshA within the sigH-rshA operon, and of sigB encoding a group 2 σ factor, supporting the previous findings of their σ(H)-dependent expression. Taken together, these results offered an additional layer of the sigma factor regulatory network in C. glutamicum. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
    Journal of Bacteriology 11/2014; 197(3). DOI:10.1128/JB.02248-14 · 2.81 Impact Factor
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    ABSTRACT: Corynebacterium glutamicum can consume glucose to excrete glycerol under oxygen deprivation. Although glycerol synthesis from 1,3-dihydroxyacetone (DHA) has been speculated, no direct evidence has yet been provided in C. glutamicum. Enzymatic and genetic investigations here indicate that the glycerol is largely produced from DHA and, unexpectedly, the reaction is catalyzed by (S,S)-butanediol dehydrogenase (ButA) that inherently catalyzes the interconversion between S-acetoin and (S,S)-2,3-butanediol. Consequently, the following pathway for glycerol biosynthesis in the bacterium emerges: dihydroxyacetone phosphate is dephosphorylated by HdpA to DHA, which is subsequently reduced to glycerol by ButA. This study emphasizes the importance of promiscuous activity of the enzyme in vivo.
    Applied Microbiology and Biotechnology 11/2014; 99(3). DOI:10.1007/s00253-014-6170-0 · 3.34 Impact Factor
  • Toru Jojima · Alain A Vertès · Masayuki Inui · Hideaki Yukawa ·
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    ABSTRACT: In conventional fermentation processes used in industrial microbiology, product formation and biomass formation often occur in parallel. The yield and cost of goods might be optimized by separating these two phenomena into two distinct phases, however. This so-called growth-arrested bioprocess can be operated particularly efficiently using cells of Corynebacterium glutamicum as biocatalysts for the production of biofuels and other commodity chemicals. Compared to traditional fermentation processes, growth-arrested bioprocesses exhibit properties that make them particularly suited to a variety of applications in lignocellulosic biorefineries. In this chapter, we describe the fundamental attributes of growth-arrested bioprocesses and review recent advances in the genetic engineering of high-performing strains tailor-designed for the production of biofuels, such as cellulosic ethanol, and commodity chemicals.
    Biorefineries: Integrated Biochemical Processes for Liquid Biofuels, 1 edited by Nasib Qureshi, David Hodge, Alain A Vertès, 08/2014: chapter 6: pages 121-139; Elsevier., ISBN: 978-0-444-59498-3
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    ABSTRACT: The transcriptional regulator GntR1 downregulates the genes for gluconate catabolism and pentose phosphate pathway in Corynebacterium glutamicum. Gluconate lowers the DNA binding affinity of GntR1, which is probably the mechanism of gluconate-dependent induction of these genes. In addition, GntR1 positively regulates ptsG, a gene encoding a major glucose transporter, and pck, a gene encoding phosphoenolpyruvate carboxykinase. Here, we searched for the new target of GntR1 on a genome-wide scale by chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis. This analysis identified 56 in vivo GntR1 binding sites, of which 7 sites were previously reported. The newly identified GntR1 sites include the upstream regions of carbon metabolism genes such as pyk, maeB, gapB, and icd, encoding pyruvate kinase, malic enzyme, glyceraldehyde 3-phosphate dehydrogenase B, and isocitrate dehydrogenase, respectively. Binding of GntR1 to the promoter region of these genes was confirmed by electrophoretic mobility shift assay. The activity of the icd, gapB, and maeB promoters was reduced by the mutation at the GntR1 binding site, in contrast to the pyk promoter activity, which was increased, indicating that GntR1 is a transcriptional activator of icd, gapB, and maeB and is a repressor of pyk. Thus, it is likely that GntR1 stimulates glucose uptake by inducing the phosphoenolpyruvate (PEP):carbohydrate phosphotransferase system (PTS) gene while repressing pyk to increase PEP availability in the absence of gluconate. Repression of zwf and gnd may reduce the NADPH supply, which may be compensated by the induction of maeB and icd. Upregulation of icd, gapB, and maeB and downregulation of pyk by GntR1 probably support gluconeogenesis.
    Journal of Bacteriology 06/2014; 196(18). DOI:10.1128/JB.01860-14 · 2.81 Impact Factor
  • Takayuki Kuge · Haruhiko Teramoto · Hideaki Yukawa · Masayuki Inui ·
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    ABSTRACT: The Corynebacterium glutamicum ATCC 31831 araBDA operon consists of three L-arabinose catabolic genes, upstream of which galM, araR, and araE genes are located in opposite orientation. araR encodes a LacI-type transcriptional regulator that negatively regulates the L-arabinose-inducible expression of araBDA and araE (encoding an L-arabionose transporter) through a mechanism yet to be identified. Here, we show that AraR protein binds in vitro to three sites, one upstream of araBDA and two upstream of araE. We verify that a 16-bp consensus palindromic sequence is essential in binding of AraR using a series of mutations introduced upstream of araB used in electrophoretic mobility shift assays. Moreover, the DNA binding activity of AraR is reduced by L-arabinose. We employ quantitative RT-PCR analyses using various mutant strains deficient in L-arabinose utilization genes to demonstrate that the prominent upregulation of araBDA and araE within 5 min of L-arabinose supplementation is dependent on the uptake but independent of the catabolism of L-arabinose. Similar expression patterns, together with the upregulation by araR disruption without L-arabinose, are evident with the apparent galM-araR operon, although attendant changes in expression levels are much smaller than those realized with the expression of araBDA and araE. The AraR-binding site upstream of araB overlaps the -10 region of the divergent galM promoter. These observations indicate that AraR acts as a transcriptional repressor of araBDA, araE, and galM-araR, and that L-arabinose acts as an intracellular negative effector of the AraR-dependent regulation.
    Journal of bacteriology 04/2014; 196(12). DOI:10.1128/JB.01655-14 · 2.81 Impact Factor
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    ABSTRACT: The qsu operon of Corynebacterium glutamicum comprises four genes (qsuABCD) that underpin the microorganism's quinate/shikimate utilization pathways. The genes encode enzymes that catalyse reactions at the metabolic branch point between the biosynthesis route for synthesis of aromatic compounds and the catabolic route for degradation of quinate and shikimate for energy production. A qsuR gene located immediately upstream of qsuA encodes a protein (QsuR) which activates the operon in the presence of quinate or shikimate. Three observations support chorismate, an intermediate of the biosynthesis route, as a direct effector of QsuR: First, induction of qsuA mRNA in the presence of either quinate or shikimate disappears upon deletion of the gene encoding chorismate synthase. Second, chorismate accumulates when the operon is induced. Third, a DNase I-protected segment by QsuR is shortened in the presence of chorismate. The QsuR tetramer senses the accumulation of chorismate and activates qsu genes that promote the quinate/shikimate catabolic instead of the aromatic compounds biosynthetic route. Such chorismate-dependent control of carbon flow has not been previously described.
    Molecular Microbiology 02/2014; 92(2). DOI:10.1111/mmi.12560 · 4.42 Impact Factor
  • Norihiko Takemoto · Yuya Tanaka · Masayuki Inui · Hideaki Yukawa ·
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    ABSTRACT: Riboflavin is a precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), which work as cofactors of numerous enzymes. Understanding the supply system of these cofactors in bacteria, particularly those used for industrial production of value added chemicals, is important given the pivotal role the cofactors play in substrate metabolism. In this work, we examined the effect of disruption of riboflavin utilization genes on cell growth, cytoplasmic flavin levels, and expression of riboflavin transporter in Corynebacterium glutamicum. Disruption of the ribA gene that encodes bifunctional GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase in C. glutamicum suppressed growth in the absence of supplemental riboflavin. The growth was fully recovered upon supplementation with 1 μM riboflavin, albeit at reduced intracellular concentrations of FMN and FAD during the log phase. Concomitant disruption of the ribA and ribM gene that encodes a riboflavin transporter exacerbated supplemental riboflavin requirement from 1 μM to 50 μM. RibM expression in FMN-rich cells was about 100-fold lower than that in FMN-limited cells. Mutations in putative FMN-riboswitch present immediately upstream of the ribM gene abolished the FMN response. This 5'UTR sequence of ribM constitutes a functional FMN-riboswitch in C. glutamicum.
    Applied Microbiology and Biotechnology 02/2014; 98(9). DOI:10.1007/s00253-014-5570-5 · 3.34 Impact Factor
  • Shogo Yamamoto · Masako Suda · Satoko Niimi · Masayuki Inui · Hideaki Yukawa ·
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    ABSTRACT: Microbial production of isobutanol is made difficult by the chemical's high cell toxicity. Corynebacterium glutamicum, inherently one of the more isobutanol-tolerant industrial microorganisms, exhibits unprecedented productivity under oxygen deprivation, potentially allowing for high productivity of such toxic chemicals as isobutanol. Here, we show that development of C. glutamicum strains proficient in isobutanol production depends not only on modulating the activity of 2-keto acid decarboxylase (KDC) and isobutanol dehydrogenase (IBDH) and suppressing by-product formation, but also on optimizing the production process to eschew product inhibition. Isobutanol production under oxygen deprivation reached 343 mM (3.2% v/v) in strain IBU5 expressing kivd (encoding KDC) under the control of ldhA promoter and adhP (encoding IBDH from Escherichia coli MG1655) under the control of gapA promoter. This productivity is double the previously reported best productivity of 1.6% (v/v) and exceeds the 2.5% (v/v) limit beyond which cell growth becomes too severely suppressed. Irrespective, a cumulative 56.5% improvement on yield was possible with the combined effects of disruption of the ppc gene, encoding phosphoenolpyruvate carboxylase (PEPC), use of a NAD(+) -specific mutant acetohydroxyacid isomeroreductase (AHAIR), and overexpression of select glycolytic genes. Using oleyl alcohol to continuously extract the isobutanol from reaction mixture and tripling the cell concentration in the reaction mixture to 60 g dry cell/L stretched the yield to 78.1% and volumetric productivity to 981 mM (9.1% v/v). Biotechnol. Bioeng. 2013;9999: 1-11. © 2013 Wiley Periodicals, Inc.
    Biotechnology and Bioengineering 11/2013; 110(11). DOI:10.1002/bit.24961 · 4.13 Impact Factor
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    Taku Nishimura · Haruhiko Teramoto · Masayuki Inui · Hideaki Yukawa ·
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    ABSTRACT: Corynebacterium glutamicum ArnR is a novel transcriptional regulator that represses expression of the nitrate reductase operon narKGHJI and the NO-detoxifying flavohemoglobin gene hmp under aerobic conditions. In a previous study we showed that the ArnR-mediated repression is relieved during anaerobic nitrate respiration but could not pinpoint the specific signal that ArnR senses. In this study, we show that in the absence of nitrate, the ArnR-mediated repression is maintained under anaerobic conditions. The derepression in response to nitrate is eliminated by disruption of narG, suggesting that ArnR senses nitrate derivatives generated during nitrate respiration. Specifically, the hmp gene is upregulated in the presence of nitrite or nitric oxide (NO) in an ArnR-dependent manner, although the response of narK appears to be greatly affected by ArnR-independent regulation. In vitro binding of ArnR to the narK and hmp promoter regions is more strongly inhibited by NO than by nitrite. We previously showed that UV-visible spectrum of ArnR is typical of a Fe-S cluster-containing protein. Site-directed mutagenesis of each of three cysteine residues, which are possibly involved in coordination of the cofactor in the ArnR protein, results in loss of the binding of this protein to its target promoters in vitro, and eliminates the repression of the target genes in vivo under aerobic conditions. These observations suggest that the cofactor coordinated by these three cysteine residues in the ArnR protein plays a critical role in the NO-responsive expression of the narKGHJI operon and hmp gene.
    Journal of bacteriology 10/2013; 196(1). DOI:10.1128/JB.01004-13 · 2.81 Impact Factor
  • Yota Tsuge · Shougo Yamamoto · Masako Suda · Masayuki Inui · Hideaki Yukawa ·
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    ABSTRACT: We previously demonstrated the simplicity of oxygen-deprived Corynebacterium glutamicum to produce D-lactate, a primary building block of next-generation biodegradable plastics, at very high optical purity by introducing heterologous D-ldhA gene from Lactobacillus delbrueckii. Here, we independently evaluated the effects of overexpressing each of genes encoding the ten glycolytic enzymes on D-lactate production in C. glutamicum. We consequently show that while the reactions catalyzed by glucokinase (GLK), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), phosphofructokinase (PFK), triosephosphate isomerase (TPI), and bisphosphate aldolase had positive effects on D-lactate productivity by increasing 98, 39, 15, 13, and 10 %, respectively, in 10 h reactions in minimal salts medium, the reaction catalyzed by pyruvate kinase had large negative effect by decreasing 70 %. The other glycolytic enzymes did not affect D-lactate productivity when each of encoding genes was overexpressed. It is noteworthy that all reactions associated with positive effects are located upstream of glycerate-1,3-bisphosphate in the glycolytic pathway. The D-lactate yield also increased by especially overexpressing TPI encoding gene up to 94.5 %. Interestingly, overexpression of PFK encoding gene reduced the yield of succinate, one of the main by-products of D-lactate production, by 52 %, whereas overexpression of GAPDH encoding gene increased succinate yield by 26 %. Overexpression of GLK encoding gene markedly increased the yield of dihydroxyacetone and glycerol by 10- and 5.8-fold in exchange with decreasing the D-lactate yield. The effect of overexpressing glycolytic genes was also evaluated in 80 h long-term reactions. The variety of effects of overexpressing each of genes encoding the ten glycolytic enzymes on D-lactate production is discussed.
    Applied Microbiology and Biotechnology 05/2013; 97(15). DOI:10.1007/s00253-013-4986-7 · 3.34 Impact Factor
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    ABSTRACT: Expression plasmids that facilitate production of bio-based products are susceptible to toxic effects that frequently affect plasmid structural stability in recombinant microbial cells. In order to enhance plasmid stability in recombinant Corynebacterium glutamicum, an expression plasmid containing genes of the Clostridium acetobutylicum butyryl-CoA synthesis operon with high structural instability within wild-type C. glutamicum was employed. From a total of 133 mutants exhibiting disruptions in 265 suspect genes, only cgR_0322-deficient mutant was able to maintain the expression plasmid intact. The mutant exhibited normal growth under standard laboratory conditions but its transformation efficiency was about one order of magnitude lower than that of wild-type strain. The cgR_0322 gene encodes an endonuclease that is active against single- as well as double-stranded DNA substrates in the presence of Mg(2+). The cgR_0322-deficient strain should therefore facilitate the development of more robust C. glutamicum strains to be used as microbial production hosts.
    Applied Microbiology and Biotechnology 05/2013; 97(18). DOI:10.1007/s00253-013-4934-6 · 3.34 Impact Factor
  • Naoko Okibe · Nobuaki Suzuki · Masayuki Inui · Hideaki Yukawa ·
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    ABSTRACT: To characterize the par system of Corynebacterium glutamicum pCGR2 and to manipulate the par components to effectively manipulate plasmid copy number. ParB binds sequence specifically to centromere-binding sites around the parAB operon and serves as an autorepressor. A small ORF (orf4, later named parC) downstream of parAB encodes a protein with 23·7% sequence identity with ParB. ParB is also implicated in the repression of parC transcription. Nonetheless, this ParC protein does not bind to centromere-binding sites and is not essential for plasmid stability. Introduction of a frameshift mutation within ParC implicated the protein in regulation of both parAB and parC. Electrophoretic Mobility Shift Assay confirmed a previously unreported ParC–ParB–parS partition complex. ParC also interacts directly with ParB without the mediation of the centromere sites. Deletion of the par components resulted in different plasmid copy numbers. A previously unreported ParC–ParB–parS partition complex is formed in pCGR2, where interaction of ParC with ParB–parS may affect the level of repression by ParB. Modifying the par components and antisense RNA enables manipulation of plasmid copy number to varying degrees. Genetically manipulating the par components, in combination with deactivation of antisense RNA, is a novel approach to artificially elevate plasmid copy number. This approach can be applied for development of new genetic engineering tools.
    Journal of Applied Microbiology 05/2013; 115(2). DOI:10.1111/jam.12257 · 2.48 Impact Factor
  • Haruhiko Teramoto · Masayuki Inui · Hideaki Yukawa ·
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    ABSTRACT: OxyR, a LysR-type transcriptional regulator, has been established as a redox-responsive activator of antioxidant genes in bacteria. This study shows that OxyR acts as a transcriptional repressor of katA, dps, ftn, and cydA in Corynebacterium glutamicum R. katA encodes H2 O2 -detoxifing enzyme catalase, dps and ftn are implicated in iron homeostasis, and cydA encodes a subunit of cytochrome bd oxidase. Quantitative RT-PCR analyses revealed that expression of katA and dps, but not of ftn and cydA, was induced by H2 O2 . Disruption of the oxyR gene encoding OxyR resulted in a marked increase in katA and dps mRNAs to a level higher than that induced by H2 O2 , and the oxyR-deficient mutant showed a H2 O2 -resistant phenotype. This is in contrast to the conventional OxyR-dependent regulatory model. ftn and cydA were also upregulated by oxyR disruption but to a smaller extent. Electrophoretic mobility shift assays revealed that the OxyR protein specifically binds to all four upstream regions of the respective genes under reducing conditions. We observed that the oxidized form of OxyR similarly bound to not only the target promoter regions but also non-specific DNA fragments. Based on these findings, we propose that the transcriptional repression by OxyR is alleviated under oxidative stress conditions in a titration mechanism due to the decreased specificity of its DNA-binding activity. DNase I footprinting analyses revealed that the OxyR-binding site in the four target promoters is approximately 50 bp in length and has multiple T-N11 -A motifs, a feature of LysR-type transcriptional regulators, but no significant overall sequence conservation. This article is protected by copyright. All rights reserved.
    FEBS Journal 04/2013; 280(14). DOI:10.1111/febs.12312 · 4.00 Impact Factor

Publication Stats

5k Citations
602.48 Total Impact Points


  • 1995-2015
    • Research Institute of Innovative Technology for the Earth
      Kioto, Kyōto, Japan
  • 2014
    • Innovative Research
      Новый, Michigan, United States
  • 2005-2011
    • Nara Institute of Science and Technology
      • Graduate School of Biological Sciences
      Ikuma, Nara, Japan
  • 2005-2007
    • University of California, Davis
      • Department of Molecular and Cellular Biology
      Davis, CA, United States
  • 2006
    • Kyushu University
      • Department of Bioscience and Biotechnology
      Fukuoka-shi, Fukuoka-ken, Japan
  • 2004
    • The University of Calgary
      • Department of Biological Sciences
      Calgary, Alberta, Canada
  • 2002
    • Mitsubishi Corp.
      Ibaragi, Ōsaka, Japan
  • 2000
    • Hungarian Academy of Sciences
      Budapeŝto, Budapest, Hungary