Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

Abstract

Small heat shock proteins (HSPs), such as HSP20, represent cellular thermal resistance mechanisms, to avoid protein aggregation at elevated temperatures. Recombinantly expressed HSP20s serve as a molecular tool for improving the tolerance of living cells to various physical and chemical stressors. Here, we aimed to heterologously express 18 HSP20s from 12 thermotolerant bacteria in Escherichia coli and evaluate their effects on various physical and chemical cellular stresses. Seventeen HSP20s were successfully expressed as soluble proteins. Recombinant E. coli cells were subjected to heat, cold, acidic, alkaline, and hyperosmolar stress to evaluate the effects of HSP20 proteins on stress resistance. Notably, the overexpression of 15 HSP20s enhanced the stress resistance of E. coli compared to that of the control strain. In particular, HSPs from Tepidimonas sediminis and Oceanithermus profundus improved the stress tolerance of E. coli under all tested conditions. In addition, E. coli harboring HSP20 from T. sediminis retained cell viability even after heat treatment at 52 °C for 5 days. To our knowledge, this is the first report of E. coli tolerance to prolonged (> 100 h) high-temperature stress. These findings indicate the potential of thermotolerant HSPs as molecular tools for improving stress tolerance in E. coli.

DOI： 10.1007/s00792-023-01326-y

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Other Link： https://link.springer.com/article/10.1007/s00792-023-01326-y/fulltext.html

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

Microbiome engineering is an emerging research field that aims to design an artificial microbiome and modulate its function. In particular, subtractive modification of the microbiome allows us to create an artificial microbiome without the microorganism of interest and to evaluate its functions and interactions with other constituent bacteria. However, few techniques that can specifically remove only a single species from a large number of microorganisms and can be applied universally to a variety of microorganisms have been developed. Antisense peptide nucleic acid (PNA) is a potent designable antimicrobial agent that can be delivered into microbial cells by conjugating with a cell-penetrating peptide (CPP). Here, we tested the efficacy of the conjugate of CPP and PNA (CPP-PNA) as microbiome modifiers. The addition of CPP-PNA specifically inhibited the growth of Escherichia coli and Pseudomonas putida in an artificial bacterial consortium comprising E. coli, P. putida, Pseudomonas fluorescens, and Lactiplantibacillus plantarum. Moreover, the growth inhibition of P. putida promoted the growth of P. fluorescens and inhibited the growth of L. plantarum. These results indicate that CPP-PNA can be used not only for precise microbiome engineering but also for analyzing the growth relationships among constituent microorganisms in the microbiome.

DOI： 10.3389/fmicb.2023.1321428

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Language：English   Publishing type：Research paper (scientific journal)  

Paraburkholderia terrae strain KU-15 grows on 2- and 4-nitrobenzoate and 2- and 4-aminobenzoate (ABA) as the sole nitrogen and carbon sources. The genes responsible for the potential degradation of 2- and 4-nitrobenzoate and 2-ABA have been predicted from its genome sequence. In this study, we identified the pab operon in P. terrae strain KU-15. This operon is responsible for the 4-ABA degradation pathway, which involves the formation of a γ-glutamylated intermediate. Reverse transcription-polymerase chain reaction revealed that the pab operon was induced by 4-ABA. Herein, studying the deletion of pabA and pabB1 in strain KU-15 and the examining of Escherichia coli expressing the pab operon revealed the involvement of the operon in 4-ABA degradation. The first step of the degradation pathway is the formation of a γ-glutamylated intermediate, whereby 4-ABA is converted to γ-glutamyl-4-carboxyanilide (γ-GCA). Subsequently, γ-GCA is oxidized to protocatechuate. Overexpression of various genes in E. coli and purification of recombinant proteins permitted the functional characterization of relevant pathway proteins: PabA is a γ-GCA synthetase, PabB1-B3 functions in a multicomponent dioxygenase system responsible for γ-GCA dioxygenation, and PabC is a γ-GCA hydrolase that reverses the formation of γ-GCA by PabA.

DOI： 10.1016/j.jbiosc.2023.11.002

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Elsevier BV  

DOI： 10.1016/j.jbiosc.2023.05.013

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Language：English   Publishing type：Research paper (scientific journal)  

Clostridioides difficile causes nosocomial antibiotic-associated diarrhea on a global scale. Susceptibility to C. difficile infection (CDI) is influenced by the composition and metabolism of gut microbiota, which in turn are affected by diet. However, the mechanism underlying the interplay between diet and gut microbiota that modulates susceptibility to CDI remains unclear. Here, we show that a soy protein diet increases the mortality of antibiotic-treated, C. difficile-infected mice while also enhancing the intestinal levels of amino acids (aas) and relative abundance of Lactobacillus genus. Indeed, Ligilactobacillus murinus-mediated fermentation of soy protein results in the generation of aas, thereby promoting C. difficile growth, and the process involves the anchored cell wall proteinase PrtP. Thus, mutual interaction between dietary protein and the gut microbiota is a critical factor affecting host susceptibility to CDI, suggesting that dietary protein sources can be an important determinant in controlling the disease.

DOI： 10.1016/j.celrep.2022.111332

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley  

DOI： 10.1002/cbic.202200210

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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/cbic.202200210

Language：English   Publishing type：Research paper (scientific journal)   Publisher：American Society for Microbiology  

Paraburkholderia terrae strain KU-15 has been investigated for its ability to degrade 2-nitrobenzoate. Here, we report the complete 10,422,345-bp genome of this microorganism, which consists of six circular replicons containing 9,483 protein-coding sequences. The genome carries genes that are potentially responsible for 2-nitrobenzoate and 4-nitirobenzoate degradation.

DOI： 10.1128/mra.00373-22

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

BACKGROUND: There has been an increasing demand for optically pure d-lactic and l-lactic acid for the production of stereocomplex-type polylactic acid. The d-lactic acid production from lignocellulosic biomass is important owing to its great abundance in nature. Corn steep liquor (CSL) is a cheap nitrogen source used for industrial fermentation, though it contains a significant amount of l-lactic acid, which decreases the optical purity of d-lactic acid produced. METHOD AND RESULTS: To remove l-lactic acid derived from the CSL-based medium, l-lactate oxidase (LoxL) from Enterococcus sp. NBRC 3427 was expressed in an engineered Lactiplantibacillus plantarum (formally called Lactobacillus plantarum) strain KOLP7, which exclusively produces d-lactic acid from both hexose and pentose sugars. When the resulting strain was applied for d-lactic acid fermentation from the mixed sugars consisting of the major constituent sugars of lignocellulose (35 g L-1 glucose, 10 g L-1 xylose, and 5 g L-1 arabinose) using the medium containing 10 g L-1 CSL, it completely removed l-lactic acid derived from CSL (0.52 g L-1 ) and produced 41.7 g L-1 of d-lactic acid. The l-lactic acid concentration was below the detection limit, and improvement in the optical purity of d-lactic acid was observed (from 98.2% to > 99.99%) by the overexpression of LoxL. CONCLUSION AND IMPLICATIONS: The LoxL-mediated consumption of l-lactic acid would enable the production of optically pure d-lactic acid in any medium contaminated by l-lactic acid.

DOI： 10.1002/biot.202100331

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Language：English   Publishing type：Research paper (scientific journal)  

The demand for the amino acid l-cysteine is increasing in the food, cosmetic, and pharmaceutical industries. Conventionally, the commercial production of l-cysteine is achieved by its extraction from the acid hydrolysate of hair and feathers. However, this production method is associated with the release of environmentally hazardous wastewater. Additionally, l-cysteine produced from animal sources cannot be halal-certified, which limits the market size. Although recent studies have developed an alternative commercial l-cysteine production method based on microbial fermentation, the production yield was insufficient owing to the cytotoxicity of l-cysteine against the host cells. In a previous study, we had developed an in vitrol-cysteine production method with a combination of 11 thermophilic enzymes, which yielded 10.5 mM l-cysteine from 20 mM glucose. In this study, we performed re-screening for enzymes catalyzing the rate-limiting steps of the in vitro pathway. Subsequently, the genes encoding enzymes necessary for the in vitro synthesis of l-cysteine were assembled in an expression vector and co-expressed in a single strain. To prevent the synthesis of hydrogen peroxide (H2O2), which is a byproduct and inhibits the enzyme activity, the redox balance in this biosynthetic pathway was maintained by replacing the H2O2-forming NADH oxidase with another enzymatic reaction in which pyruvate was used as a sacrificial substrate. The re-designed in vitro synthetic pathway resulted in the production of 28.2 mM l-cysteine from 20 mM glucose with a molar yield of 70.5%.

DOI： 10.1016/j.jbiosc.2021.09.003

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system is a valuable genome editing tool for microorganisms. However, the commonly used Cas9 nuclease derived from Streptococcus pyogenes (SpCas9) is not applicable to many industrially relevant bacteria, due to its cytotoxicity and large size (1368 amino acids [aa]). We developed an alternative genome editing system using a miniature Cas12f1 nuclease (529 aa) derived from an uncultured archaeon, Un1Cas12f1. When editing four dispensable genes in Escherichia coli MG1655 and BW25113, the CRISPR/Un1Cas12f1 system showed higher efficiency (63%-100%) than the CRISPR/SpCas9 system (50%-79%). The CRISPR/Un1Cas12f1 genome editing system is expected to be applied to the genome editing of a wide variety of bacteria.

DOI： 10.1016/j.jbiosc.2021.04.009

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Coenzyme A (CoA) is an essential cofactor present in all domains of life and is involved in numerous metabolic pathways, including fatty acid metabolism, pyruvate oxidation through the TCA cycle, and production of secondary metabolites. This characteristic makes CoA a commercially valuable compound in the pharmaceutical, cosmetic, and clinical industries. However, CoA is difficult to accumulate in living cells at a high level as it is consumed in multiple metabolic pathways, hampering its manufacturing by typical cell cultivation and extraction approaches. The feedback inhibition by CoA to a biosynthetic enzyme, pantothenate kinase (PanK), is also a serious obstacle for high-titer production of CoA. To overcome this challenge, in vitro production of CoA, in which the CoA biosynthetic pathway was reconstructed outside of cells using recombinant thermophilic enzymes, was performed. The in vitro pathway was designed to be insensitive to the feedback inhibition of CoA using a CoA-insensitive type-III PanK from the thermophilic bacterium Thermus thermophilus Furthermore, a statistical approach using Design of Experiments was employed to rationally determine the enzyme loading ratio to maximize CoA production rate. Consequently, 0.94 mM CoA could be produced from 2 mM d-pantetheine through the designed pathway. We hypothesized that the insufficient conversion yield is attributed to the high Km value of T. thermophilus PanK towards ATP. Based on these observations, possible CoA regulation mechanisms in T. thermophilus and approaches to improve the feasibility of CoA production through the in vitro pathway have been investigated.IMPORTANCEThe biosynthesis of coenzyme A (CoA) in bacteria and eukaryotes is regulated by feedback inhibition targeting type-I and type-II pantothenate kinase (PanK). Type-III PanK is only found in bacteria and is generally insensitive to CoA. Previously, type-III PanK from the hyperthermophilic bacterium Thermotoga maritima was shown to defy this typical characteristic, and instead shows inhibition towards CoA. In the present study, phylogenetic analysis combined with functional analysis of type-III PanK from thermophiles revealed that the CoA-sensitive behavior of type-III PanK from T. maritima is uncommon. We cloned type-III PanKs from Thermus thermophilus and Geobacillus sp. 30 and showed that neither enzyme's activities were inhibited by CoA. Furthermore, we utilized type-III PanK for a one-pot cascade reaction to produce CoA.

DOI： 10.1128/AEM.00541-21

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Springer Science and Business Media LLC  

DOI： 10.1007/s00792-021-01238-9

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Other Link： https://link.springer.com/article/10.1007/s00792-021-01238-9/fulltext.html

Language：English   Publishing type：Research paper (scientific journal)  

Cupriavidus necator strain A-04 has shown 16S rRNA gene identity to the well-known industrial strain C. necator H16. Nevertheless, the cell characteristics and polyhydroxyalkanoate (PHA) production ability of C. necator strain A-04 were different from those of C. necator H16. This study aimed to express PHA biosynthesis genes of C. necator strain A-04 in Escherichia coli via an arabinose-inducible expression system. In this study, the PHA biosynthesis operon of C. necator strain A-04, consisting of three genes encoding acetyl-CoA acetyltransferase (phaAA-04, 1182 bp, 40.6 kDa), acetoacetyl-CoA reductase (phaBA-04, 741 bp, 26.4 kDa) and PHB synthase Class I (phaCA-04, 1770 bp), was identified. Sequence analysis of the phaAA-04, phaBA-04, and phaCA-04 genes revealed that phaCA-04 was 99% similar to phaCH16 from C. necator H16. The difference in amino acid residue situated at position 122 of phaCA-04 was proline, whereas that of C. necator H16 was leucine. The intact phaCABA-04 operon was cloned into the arabinose-inducible araBAD promoter and transformed into E. coli strains Top 10, JM109 and XL-1 blue. The results showed that optimal conditions obtained from shaken flask experiments yielded 6.1 ± 1.1 g/L cell dry mass (CDM), a PHB content of 93.3 ± 0.9% (w/w) and a productivity of 0.24 g/(L⋅h), whereas the wild-type C. necator strain A-04 accumulated 78% (w/w) PHB with a productivity of 0.09 g/(L⋅h). Finally, for the scaled-up studies, fed-batch cultivations by pH-stat control in a 5-L fermenter of E. coli strains XL1-Blue harboring pBAD/Thio-TOPO-phaCABA-04 and pColdTF-phaCABA-04 in MR or LB medium, leading to a PHB production of 31.4 ± 0.9 g/L at 54 h with a PHB content of 83.0 ± 3.8% (w/w), a CDM of 37.8 ± 1.2 g/L, a Y
P/S
value of 0.39 g PHB/g glucose and a productivity of 0.6 g PHB/(L⋅h) using pColdTF-phaCABA-04 in MR medium. In addition, PHB production was 29.0 ± 1.1 g/L with 60.2 ± 2.3% PHB content in the CDM of 53.1 ± 1.0 g/L, a Y
P/S
value of 0.21 g PHB/g glucose and a productivity of 0.4 g PHB/(L⋅h) using pBAD/Thio-TOPO-phaCABA-04 in LB medium. Thus, a relatively high PHB concentration and productivity were achieved, which demonstrated the possibility of industrial production of PHB.

DOI： 10.3389/fbioe.2021.661096

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Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：MDPI AG  

S-Adenosylmethionine (SAM)-dependent methyltransferases are important tools for the biocatalytic methylation of diverse biomolecules. Methylation by a whole-cell biocatalyst allows the utilization of intrinsic SAM and its regeneration system, which consists of a cyclic and multi-step enzymatic cascade. However, low intracellular availability of 5-methyl-tetrahydrofolate (5-methyl-THF), which functions as a methyl group donor, limits SAM regeneration. Here, we integrated methanol metabolism with 5-methyl-THF formation into SAM-dependent methylation system in Escherichia coli, driven by heterologously expressed methanol dehydrogenase (MDH). The coupling of MDH-catalyzed methanol oxidation with the E. coli endogenous reactions enhances the formation of 5-methyl-THF using methanol as a source of methyl group, thereby promoting both the SAM regeneration and methylation reactions. Co-expression of the mutant MDH2 from Cupriavidus necator N-1 with the O-methyltransferase 5 from Streptomyces avermitilis MA-4680 enhanced O-methylation of esculetin 1.4-fold. Additional overexpression of the E. coli endogenous 5,10-methylene-THF reductase, which catalyzes the last step of 5-methyl-THF formation, further enhanced the methylation reaction by 1.9-fold. Together with deregulation of SAM biosynthesis, the titer of methylated compounds was increased about 20-fold (from 0.023 mM to 0.44 mM). The engineered E. coli strain with enhanced 5-methyl-THF formation is now available as a chassis strain for the production of a variety of methylated compounds.

DOI： 10.3390/catal10091001

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Authorship：Lead author,　Corresponding author   Language：English  

In vitro metabolic engineering is an emerging framework for bioproduction systems, in which synthetic metabolic pathways are constructed using a limited number of enzymes. Employment of thermophilic enzymes as catalytic elements in pathways enables the use of simple heat purification of recombinantly expressed enzymes. However, thermophilic enzymes are generally incompatible with thermo-labile substrates and intermediates. In previous work, we showed that lactate production through a non-ATP forming chimeric Embden-Meyerhof (EM) pathway required careful adjustment of the metabolic fluxes by continuous substrate feeding and optimization of enzyme ratios to prevent the accumulation and degradation of thermo-labile intermediates (Ye et al., Microb. Cell Fact., 11, 120, 2012). In the study reported here, we constructed an in vitro non-phosphorylative Entner-Doudoroff (np-ED) pathway. Because of the high thermal stability of the metabolic intermediates in the np-ED pathway, it could prevent degradation of accumulated metabolic intermediates caused by inconstant metabolic fluxes, and batch-mode production of lactate in which the concentrations of the substrate and metabolic intermediates change dynamically could be achieved. By combining the enzymes involved in the np-ED pathway and lactate dehydrogenase, 20.9 mM lactate was produced from 10 mM glucose and 1 mM gluconate in 6 h.

DOI： 10.1016/j.jbiosc.2019.09.010

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Language：English   Publishing type：Research paper (scientific journal)  

Growth temperature is one of the most representative biological parameters for characterizing living organisms. Prokaryotes have been isolated from various temperature environments and show wide diversity in their growth temperatures. We herein constructed a database of growth TEMPeratures of Usual and RAre prokaryotes (TEMPURA, http://togodb.org/db/tempura), which contains the minimum, optimum, and maximum growth temperatures of 8,639 prokaryotic strains. Growth temperature information is linked with taxonomy IDs, phylogenies, and genomic information. TEMPURA provides useful information to researchers working on biotechnological applications of extremophiles and their biomolecules as well as those performing fundamental studies on the physiological diversity of prokaryotes.

DOI： 10.1264/jsme2.ME20074

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Cysteine is a commercially valuable amino acid with an increasing demand in the food, cosmetic, and pharmaceutical industries. Although cysteine is conventionally manufactured by extraction from animal proteins, this method has several problems, such as troublesome waste-water treatment and incompatibility with some dietary restrictions. Fermentative production of cysteine from plant-derived substrates is a promising alternative for the industrial production of cysteine. However, it often suffers from low product yield as living organisms are equipped with various regulatory systems to control the intracellular cysteine concentration at a moderate level. In this study, we constructed an in vitro cysteine biosynthetic pathway by assembling 11 thermophilic enzymes. The in vitro pathway was designed to be insensitive to the feedback regulation by cysteine and to balance the intra-pathway consumption and regeneration of cofactors. A kinetic model for the in vitro pathway was built using rate equations of individual enzymes and used to optimize the loading ratio of each enzyme. Consequently, 10.5 mM cysteine could be produced from 20 mM glucose through the optimized pathway. However, the observed yield and production rate of the assay were considerably lower than those predicted by the model. Determination of cofactor concentrations in the reaction mixture indicated that the inconsistency between the model and experimental assay could be attributed to the depletion of ATP and ADP, likely due to host-derived, thermo-stable enzyme(s). Based on these observations, possible approaches to improve the feasibility of cysteine production through an in vitro pathway have been discussed.

DOI： 10.1007/s00253-019-10061-4

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DOI： 10.1186/s12934-019-1125-x

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DOI： 10.1016/j.jbiosc.2018.07.011

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DOI： 10.1093/femsle/fny215

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Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)   Publisher：Wiley-VCH Verlag  

DOI： 10.1002/biot.201700517

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DOI： 10.1007/s13280-017-0976-9

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DOI： 10.1016/j.jbiosc.2017.04.013

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DOI： 10.1128/JB.00359-17

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Language：English   Publisher：KeAi Communications Co.  

DOI： 10.1016/j.synbio.2017.06.002

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DOI： 10.1016/j.jbiosc.2017.01.016

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DOI： 10.1007/s00253-016-7976-8

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DOI： 10.1016/j.seppur.2016.06.040

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DOI： 10.1016/j.seppur.2016.03.054

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DOI： 10.1016/j.ymben.2016.02.005

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DOI： 10.1371/journal.pone.0146146

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DOI： 10.1016/j.seppur.2015.01.043

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DOI： 10.1002/bit.25338

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DOI： 10.1007/s00253-014-5668-9

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Language：English   Publishing type：Part of collection (book)   Publisher：Wiley Blackwell  

DOI： 10.1002/9781118845394.ch13

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DOI： 10.1016/j.jbiosc.2013.07.005

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DOI： 10.1186/1475-2859-12-91

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DOI： 10.1016/j.watres.2013.01.052

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DOI： 10.1016/j.jbiotec.2012.11.011

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DOI： 10.1128/AEM.03752-12

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Language：English   Publishing type：Research paper (scientific journal)   Publisher：Academic Press Inc.  

DOI： 10.1016/j.ymben.2013.09.006

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DOI： 10.1186/1475-2859-11-120

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DOI： 10.1271/bbb.120362

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DOI： 10.1016/j.jbiosc.2011.11.016

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DOI： 10.1016/j.bej.2011.08.002

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DOI： 10.1007/s00253-011-3356-6

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DOI： 10.1007/s00253-011-3342-z

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DOI： 10.1007/s00253-009-2280-5

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DOI： 10.1007/s00253-009-2111-8

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DOI： 10.1128/AEM.01692-09

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DOI： 10.1128/AEM.00573-09

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DOI： 10.1128/AEM.01514-08

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DOI： 10.1128/AEM.02012-07

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DOI： 10.1007/s00253-007-0905-0

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DOI： 10.1007/s00253-006-0477-4

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DOI： 10.1007/s00253-005-0111-x

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DOI： 10.1128/AEM.72.1.269-275.2006

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Total pages：776   Responsible for pages：519-524  

ASIN

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Language：Japanese   Publisher：農林水産・食品産業技術振興協会  

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Language：Japanese   Publisher：化学工業社  

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Language：Japanese   Publisher：日本生物工学会  

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Language：Japanese   Publisher：公益社団法人 日本農芸化学会  

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Language：Japanese   Publisher：日本生物工学会  

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Language：Japanese   Publisher：日本バイオプラスチック協会  

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Language：Japanese   Publisher：日本生物工学会  

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Language：English   Presentation type：Oral presentation (invited, special)  

Venue：Chuncheon, Korea  

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Venue：Chiayi, Taiwan  

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Venue：Keio University, Kanagawa  

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Venue：Tokushima University, Tokushima  

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Language：Japanese   Presentation type：Symposium, workshop panel (nominated)  

Venue：徳島大学  

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Language：English   Presentation type：Poster presentation  

Venue：Philadelphia, USA  

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Venue：Osaka  

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Language：English   Presentation type：Poster presentation  

Venue：Kaohsiung, Taiwan  

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