JBB : Journal of Bioscience and Bioengineering

            

Journal of Bioscience and Bioengineering vol.122 cover

 



  • Exploring the proteomic characteristics of the Escherichia coli B and K-12 strains in different cellular compartments
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Mee-Jung Han

    Escherichia coli, one of the well-characterized prokaryotes, has been the most widely used bacterial host in scientific studies and industrial applications. Many different strains have been developed for the widespread use of E. coli in biotechnology, and selecting an ideal host to produce a specific protein of interest is a critical step in developing a production process. The E. coli B and K-12 strains are among the most frequently used bacterial hosts for the production of recombinant proteins as well as small-molecule metabolites such as amino acids, biofuels, carboxylic acids, diamines, and others. However, both strains have distinctive differences in genotypic and phenotypic attributes, and their behaviors can still be unpredictable at times, especially while expressing a recombinant protein. Therefore, in this review, an in-depth analysis of the physiological behavior on the proteomic level was performed, wherein the particularly distinct proteomic differences between the E. coli B and K-12 strains were investigated in the four distinctive cellular compartments. Interesting differences in the proteins associated with key cellular properties including cell growth, protein production and quality, cellular tolerance, and motility were observed between the two representative strains. The resulting enhancement of knowledge regarding host physiology that is summarized herein is expected to contribute to the acceleration of strain improvements and optimization for biotechnology-related processes.





  • Enhancement of 5-keto-d-gluconate production by a recombinant Gluconobacter oxydans using a dissolved oxygen control strategy
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Jianfeng Yuan, Mianbin Wu, Jianping Lin, Lirong Yang

    The rapid and incomplete oxidation of sugars, alcohols, and polyols by the gram-negative bacterium Gluconobacter oxydans facilitates a wide variety of biological applications. For the conversion of glucose to 5-keto-d-gluconate (5-KGA), a promising precursor of the industrial substance L-(+)-tartaric acid, G. oxydans DSM2343 was genetically engineered to strain ZJU2, in which the GOX1231 and GOX1081 genes were knocked out in a markerless fashion. Then, a secondary alcohol dehydrogenase (GCD) from Xanthomonas campestris DSM3586 was heterologously expressed in G. oxydans ZJU2. The 5-KGA production and cell yield were increased by 10% and 24.5%, respectively. The specific activity of GCD towards gluconate was 1.75±0.02 U/mg protein, which was 7-fold higher than that of the sldAB in G. oxydans. Based on the analysis of kinetic parameters including specific cell growth rate (μ), specific glucose consumption rate (q s ) and specific 5-KGA production rate (q p ), a dissolved oxygen (DO) control strategy was proposed. Finally, batch fermentation was carried out in a 15-L bioreactor using an initial agitation speed of 600 rpm to obtain a high μ for cell growth. Subsequently, DO was continuously maintained above 20% to achieve a high q p to ensure a high accumulation of 5-KGA. Under these conditions, the maximum concentration of 5-KGA reached 117.75 g/L with a productivity of 2.10 g/(L·h).





  • Improvement of ethanol production by recombinant expression of pyruvate decarboxylase in the white-rot fungus Phanerochaete sordida YK-624
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Jianqiao Wang, Sho Hirabayashi, Toshio Mori, Hirokazu Kawagishi, Hirofumi Hirai

    To improve ethanol production by Phanerochaete sordida YK-624, the pyruvate decarboxylase (PDC) gene was cloned from and reintroduced into this hyper lignin-degrading fungus; the gene encodes a key enzyme in alcoholic fermentation. We screened 16 transformant P. sordida YK-624 strains that each expressed a second, recombinant PDC gene (pdc) and then identified the transformant strain (designated GP7) with the highest ethanol production. Direct ethanol production from hardwood was 1.41 higher with GP7 than with wild-type P. sordida YK-624. RT-PCR analysis indicated that the increased PDC activity was caused by elevated recombinant pdc expression. Taken together, these results suggested that ethanol production by P. sordida YK-624 can be improved by the stable expression of an additional, recombinant pdc.





  • Microbial production of dihomo-γ-linolenic acid by Δ5-desaturase gene-disruptants of Mortierella alpina 1S-4
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Hiroshi Kikukawa, Eiji Sakuradani, Akinori Ando, Tomoyo Okuda, Sakayu Shimizu, Jun Ogawa

    We constructed dihomo-γ-linolenic acid (DGLA)-producing strains with disruption of the Δ5-desaturase (Δ5ds) gene, which encodes a key enzyme catalyzing the bioconversion of DGLA to arachidonic acid (ARA), by efficient gene-targeting, using Δlig4 strain of Mortierella alpina 1S-4 as the host. In previous study, we had already identified and disrupted the lig4 gene encoding DNA ligase 4, which involves in non-homologous end joining, in M. alpina 1S-4, and the Δlig4 strain had showed efficient gene-targeting. In this study, the uracil auxotroph of Δlig4 strain was constructed, and then transformed for disruption of Δ5ds. The isolation of nine Δ5ds-disruptants out of 18 isolates indicated that the disruption efficiency was 50%. The ratio of DGLA among the total fatty acids of the Δ5ds-disruptants reached 40.1%; however, no ARA was detected. To our knowledge, this is the first study to report the construction of DGLA-producing transformants by using the efficient gene-targeting system in M. alpina 1S-4.





  • Characterization and expression of the antifungal protein from Monascus pilosus and its distribution among various Monascus species
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Ching-Yu Tu, Yu-Pei Chen, Ming-Chen Yu, Ing-Er Hwang, Dai-Ying Wu, Li-Ling Liaw

    Monascus species are traditionally used for food preservation. This study used the disc diffusion method to verify the antifungal activity of protein extracted from Monascus pilosus BCRC38072 against 15 fungal pathogens. An antifungal protein, designated as MAFP1, was successfully purified and confirmed through N-terminal sequencing. To further explore the antifungal gene, a mafp1 gene that is similar to that of PgAFP from Penicillium chrysogenum was cloned from M. pilosus BCRC38072. According to the N-terminal sequencing and in silico analysis, the signal peptide was assumed to have 18 amino acids and the mature MAFP1 to contain 58 peptides. Moreover, the mafp1 gene was recognized in Monascus ruber, Monascus barkeri, Monascus floridanus, and Monascus lunisporas through polymerase chain reaction and DNA sequencing and showed high homology. By contrast, the mafp1 gene was absent in Monascus kaoliang, Monascus purpureus, and Monascus sanguineus. In addition, the mafp1 gene with N-terminal polyhistidine fusion was overexpressed in Escherichia coli. However, the antifungal activity of recombinant MAFP1 was significantly lower than that of native MAFP1. According to the properties of MAFP1, Monascus species may have food preservation applications.





  • Overexpressing enzymes of the Ehrlich pathway and deleting genes of the competing pathway in Saccharomyces cerevisiae for increasing 2-phenylethanol production from glucose
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Li Shen, Yuya Nishimura, Fumio Matsuda, Jun Ishii, Akihiko Kondo

    2-Phenylethanol (2-PE) is a higher aromatic alcohol that is used in the cosmetics and food industries. The budding yeast Saccharomyces cerevisiae is considered to be a suitable host for the industrial production of higher alcohols, including 2-PE. To produce 2-PE from glucose in S. cerevisiae, we searched for suitable 2-keto acid decarboxylase (KDC) and alcohol dehydrogenase (ADH) enzymes of the Ehrlich pathway for overexpression in strain YPH499, and found that overexpression of the ARO10 and/or ADH1 genes increased 2-PE production from glucose. Further, we screened ten BY4741 single-deletion mutants of genes involved in the competing pathways for 2-PE production, and found that strains aro8Δ and aat2Δ displayed increased 2-PE production. Based on these results, we engineered a BY4741 strain that overexpressed ARO10 and contained an aro8Δ deletion, and demonstrated that the strain produced 96 mg/L 2-PE from glucose as the sole carbon source. As this engineered S. cerevisiae strain showed a significant increase in 2-PE production from glucose without the addition of an intermediate carbon substrate, it is a promising candidate for the large-scale production of 2-PE.





  • Rapamycin-induced oligomer formation system of FRB–FKBP fusion proteins
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Tomonao Inobe, Nobuyuki Nukina

    Most proteins form larger protein complexes and perform multiple functions in the cell. Thus, artificial regulation of protein complex formation controls the cellular functions that involve protein complexes. Although several artificial dimerization systems have already been used for numerous applications in biomedical research, cellular protein complexes form not only simple dimers but also larger oligomers. In this study, we showed that fusion proteins comprising the induced heterodimer formation proteins FRB and FKBP formed various oligomers upon addition of rapamycin. By adjusting the configuration of fusion proteins, we succeeded in generating an inducible tetramer formation system. Proteins of interest also formed tetramers by fusing to the inducible tetramer formation system, which exhibits its utility in a broad range of biological applications.





  • Characterization of a trehalose-degrading enzyme from the hyperthermophilic archaeon Sulfolobus acidocaldarius
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Jeong Hyun Moon, Whiso Lee, Jihee Park, Kyoung-Hwa Choi, Jaeho Cha

    We purified a cytosolic trehalase (TreH) from a thermoacidophilic archaeon Sulfolobus acidocaldarius. Enzyme activity in cell-free extracts indicated that trehalose degradation in the cell occurred via the hydrolytic activity of TreH, and not via TreP (phosphorolytic activity) or TreT (transfer activity). TreH was purified to near-homogeneity by DEAE anion-exchange chromatography, followed by size exclusion and HiTrap Q anion-exchange chromatography, and its molecular mass was estimated as 40 kDa. Maximum activity was observed at 85°C and pH 4.5. The half-life of TreH was 53 and 41 min at 90°C and 95°C, respectively. TreH was highly specific for trehalose and was inhibited by glucose with a K i of 0.05 mM. Compared with TreH from other trehalases, TreH from S. acidocaldarius is the most thermostable trehalase reported so far. Furthermore, this is the first trehalase characterized in the Archaea domain.





  • Maximum-biomass prediction of homofermentative Lactobacillus
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Shumao Cui, Jianxin Zhao, Xiaoming Liu, Yong Q. Chen, Hao Zhang, Wei Chen

    Fed-batch and pH-controlled cultures have been widely used for industrial production of probiotics. The aim of this study was to systematically investigate the relationship between the maximum biomass of different homofermentative Lactobacillus and lactate accumulation, and to develop a prediction equation for the maximum biomass concentration in such cultures. The accumulation of the end products and the depletion of nutrients by various strains were evaluated. In addition, the minimum inhibitory concentrations (MICs) of acid anions for various strains at pH 7.0 were examined. The lactate concentration at the point of complete inhibition was not significantly different from the MIC of lactate for all of the strains, although the inhibition mechanism of lactate and acetate on Lactobacillus rhamnosus was different from the other strains which were inhibited by the osmotic pressure caused by acid anions at pH 7.0. When the lactate concentration accumulated to the MIC, the strains stopped growing. The maximum biomass was closely related to the biomass yield per unit of lactate produced (Y X/P ) and the MIC (C) of lactate for different homofermentative Lactobacillus. Based on the experimental data obtained using different homofermentative Lactobacillus, a prediction equation was established as follows: X max − X 0 = (0.59 ± 0.02)·Y X/P ·C.





  • Development of flocculent Saccharomyces cerevisiae strain GYK-10 for the selective fermentation of glucose/fructose in sugar mills
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Taku Kato, Satoshi Ohara, Yasuhiro Fukushima, Akira Sugimoto, Takayuki Masuda, Takaomi Yasuhara, Hiromi Yamagishi

    Advances in glucose/fructose-selective ethanol production have successfully enhanced raw sugar extraction from sugarcane juice by converting inhibitory substances (i.e., glucose/fructose) into ethanol, which is removed by subsequent operations in cane sugar mills. However, the commercial implementation of this breakthrough process in existing cane sugar mills requires a yeast strain that (i) can be used in food production processes, (ii) exhibits stable saccharometabolic selectivity, and (iii) can be easily separated from the saccharide solution. In this study, we developed a suitable saccharometabolism-selective and flocculent strain, Saccharomyces cerevisiae GYK-10. We obtained a suitable yeast strain for selective fermentation in cane sugar mills using a yeast mating system. First, we crossed a haploid strain defective in sucrose utilization with a flocculent haploid strain. Next, we performed tetrad dissection of the resultant hybrid diploid strain and selected GYK-10 from various segregants by investigating the sucrose assimilation and flocculation capacity phenotypes. Ten consecutive fermentation tests of the GYK-10 strain using a bench-scale fermentor confirmed its suitability for the implementation of practical selective fermentation in a commercial sugar mill. The strain exhibited complete saccharometabolic selectivity and sustained flocculation, where it maintained a high ethanol yield and conversion rate throughout the test.





  • Experimental evolution and gene knockout studies reveal AcrA-mediated isobutanol tolerance in Ralstonia eutropha
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Amanda C. Bernardi, Claudia S. Gai, Jingnan Lu, Anthony J. Sinskey, Christopher J. Brigham

    Isobutanol (IBT) has attracted much attention from researchers as a next generation drop-in biofuel. Ralstonia eutropha is a gram-negative bacterium which naturally produces polyhydroxybutyrate (PHB), and has been reported to produce IBT after metabolic engineering. Similar to other microbes, R. eutropha experiences toxicity from branched-chain alcohols and is unable to grow in the presence of IBT concentrations higher than 0.5% (v v−1). Such low tolerance greatly limits the ability of R. eutropha to grow and produce IBT. In order to study toxicity to the cells, IBT-tolerant strains were developed by experimental evolution, revealing that two genes, previously described as being related to IBT tolerance in Escherichia coli (acrA and acrA6), also presented mutations in R. eutropha evolved strains. The effect on the physiology of the cells of in-frame deletions of each of these genes was assessed in wild type and engineered IBT-producing strains in an attempt to reproduce a tolerant phenotype. The mutant strains' ability to tolerate, consume, and produce IBT were also analyzed. Although deletions of acrA6 and acrA did not significantly improve R. eutropha growth in the presence of IBT, these deletions improved cell survival in the presence of high concentrations of IBT in the extracellular milieu. Moreover, an in-frame acrA deletion in an engineered IBT-producing R. eutropha enhanced the strain's ability to produce IBT, which could potentially be associated with enhanced survival at high IBT concentrations.





  • The relationship between rice protein composition and nitrogen compounds in sake
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Masaki Okuda, Minami Miyamoto, Midori Joyo, Kei Takahashi, Nami Goto-Yamamoto, Shuichi Iida, Takuro Ishii

    The relationship between the protein composition of rice and nitrogen compounds (amino acids and oligo-peptides) in the produced sake were investigated using endosperm protein mutant rice (LGC-1, LGC-Jun, Kx433, QA28), sake rice (Yamadanishiki) and cooking rice (Nipponbare, Nihonmasari, Koshihikari). The total nitrogen concentration, amino acid concentration and most peptide peak areas determined by RP-HPLC and gel filtration chromatography of the produced sake were lower when sake was made from a low glutelin content rice mutant compared with other rice varieties. The concentration of nitrogen compounds in the sake positively correlated with the glutelin content of the highly milled rice grains used for sake production. Sake produced using a low glutelin content rice mutant is generally evaluated as having a light taste. Our findings suggest that nitrogen compounds (oligo-peptides and amino acids) derived from rice glutelin significantly contribute to the taste of sake.





  • Quantification of coffee blends for authentication of Asian palm civet coffee (Kopi Luwak) via metabolomics: A proof of concept
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Udi Jumhawan, Sastia Prama Putri, Yusianto, Takeshi Bamba, Eiichiro Fukusaki

    Asian palm civet coffee (Kopi Luwak), an animal-digested coffee with an exotic feature, carries a notorious reputation of being the rarest and most expensive coffee beverage in the world. Considering that illegal mixture of cheap coffee into civet coffee is a growing concern among consumers, we evaluated the use of metabolomics approach and orthogonal projection to latent structures (OPLS) prediction technique to quantify the degree of coffee adulteration. Two prediction sets, consisting of certified and commercial coffee, were made from a blend of civet and regular coffee with eleven mixing percentages. The prediction model exhibited accurate estimation of coffee blend percentage thus, successfully validating the prediction and quantification of the mixing composition of known–unknown samples. This work highlighted proof of concept of metabolomics application to predict degree of coffee adulteration by determining the civet coffee fraction in blends.





  • Enhanced denitrification of Pseudomonas stutzeri by a bioelectrochemical system assisted with solid-phase humin
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Zhixing Xiao, Takanori Awata, Dongdong Zhang, Chunfang Zhang, Zhiling Li, Arata Katayama

    The denitrification reactions performed by Pseudomonas stutzeri JCM20778 were enhanced electrochemically with the use of solid-phase humin, although P. stutzeri itself was incapable of receiving electrons directly from the graphite electrode. Electrochemically reduced humin enhanced the microbial, but not abiotic, denitrification reactions. Electric current and cyclic voltammetry analyses suggested that the solid-phase humin functioned as an electron donor for the denitrification reactions of P. stutzeri. Nitrogen balance study and the estimation of the first-order rate constants of the consecutive denitrification reactions suggested that the solid-phase humin enhanced all reducing reactions from nitrate to nitrogen gas. Considering the wide distribution of humin in the environment, the findings that solid-phase humin can assist in electron transfer, from the electrode to a denitrifying bacterium that has little ability to directly utilize external electrons, has important implications for the widespread application of bioelectrochemical systems assisted by solid-phase humin for enhancing microbial denitrification.





  • Characterization of Fe (III)-reducing enrichment culture and isolation of Fe (III)-reducing bacterium Enterobacter sp. L6 from marine sediment
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Hongyan Liu, Hongyu Wang

    To enrich the Fe (III)-reducing bacteria, sludge from marine sediment was inoculated into the medium using Fe (OH)3 as the sole electron acceptor. Efficiency of Fe (III) reduction and composition of Fe (III)-reducing enrichment culture were analyzed. The results indicated that the Fe (III)-reducing enrichment culture with the dominant bacteria relating to Clostridium and Enterobacter sp. had high Fe (III) reduction of (2.73 ± 0.13) mmol/L-Fe (II). A new Fe (III)-reducing bacterium was isolated from the Fe (III)-reducing enrichment culture and identified as Enterobacter sp. L6 by 16S rRNA gene sequence analysis. The Fe (III)-reducing ability of strain L6 under different culture conditions was investigated. The results indicated that strain L6 had high Fe (III)-reducing activity using glucose and pyruvate as carbon sources. Strain L6 could reduce Fe (III) at the range of NaCl concentrations tested and had the highest Fe (III) reduction of (4.63 ± 0.27) mmol/L Fe (II) at the NaCl concentration of 4 g/L. This strain L6 could reduce Fe (III) with unique properties in adaptability to salt variation, which indicated that it can be used as a model organism to study Fe (III)-reducing activity isolated from marine environment.





  • Changes in bacterial community structure in a full-scale membrane bioreactor for municipal wastewater treatment
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Kurumi Hashimoto, Hirofumi Tsutsui, Kazuki Takada, Hiroshi Hamada, Kousuke Sakai, Daisuke Inoue, Kazunari Sei, Satoshi Soda, Kyoko Yamashita, Koji Tsuji, Toshikazu Hashimoto, Michihiko Ike

    This study investigated changes in the structure and metabolic capabilities of the bacterial community in a full-scale membrane bioreactor (MBR) treating municipal wastewater. Microbial monitoring was also conducted for a parallel-running conventional activated sludge (CAS) process treating the same influent. The mixed-liquor suspended solid concentration in the MBR reached a steady-state on day 73 after the start-up. Then the MBR maintained higher rates of removal of organic compounds and nitrogen than the CAS process did. Terminal restriction fragment length polymorphism analysis revealed that the bacterial community structure in the MBR was similar to that in the CAS process at the start-up, but it became very different from that in the CAS process in the steady state. The bacterial community structure of the MBR continued to change dynamically even after 20 months of the steady-state operation, while that of the CAS process was maintained in a stable condition. By contrast, Biolog assay revealed that the carbon source utilization potential of the MBR resembled that of the CAS process as a whole, although it declined transiently. Overall, the results indicate that the bacterial community of the MBR has flexibility in terms of its phylogenetic structure and metabolic activity to maintain the high wastewater treatment capability.





  • Simultaneous production of l-lactic acid with high optical activity and a soil amendment with food waste that demonstrates plant growth promoting activity
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Vichien Kitpreechavanich, Arisa Hayami, Anfal Talek, Clament Fui Seung Chin, Yukihiro Tashiro, Kenji Sakai

    A unique method to produce highly optically-active l-lactic acid and soil amendments that promote plant growth from food waste was proposed. Three Bacillus strains Bacillus subtilis KBKU21, B. subtilis N3-9 and Bacillus coagulans T27, were used. Strain KBKU21 accumulated 36.9 g/L l-lactic acid with 95.7% optical activity and 98.2% l-lactic acid selectivity when fermented at 43°C for 84 h in a model kitchen refuse (MKR) medium. Residual precipitate fraction (anaerobically-fermented MKR (AFM) compost) analysis revealed 4.60%, 0.70% and 0.75% of nitrogen (as N), phosphorous (as P2O5), and potassium (as K2O), respectively. Additionally, the carbon to nitrogen ratio decreased from 13.3 to 10.6. AFM compost with KBKU21 promoted plant growth parameters, including leaf length, plant height and fresh weight of Brassica rapa (Komatsuna), than that by chemical fertilizers or commercial compost. The concept provides an incentive for the complete recycling of food waste, contributing towards a sustainable production system.





  • Web application for genetic modification flux with database to estimate metabolic fluxes of genetic mutants
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Noorlin Mohd Ali, Ryo Tsuboi, Yuta Matsumoto, Daisuke Koishi, Kentaro Inoue, Kazuhiro Maeda, Hiroyuki Kurata

    Computational analysis of metabolic fluxes is essential in understanding the structure and function of a metabolic network and in rationally designing genetically modified mutants for an engineering purpose. We had presented the genetic modification flux (GMF) that predicts the flux distribution of a broad range of genetically modified mutants. To enhance the feasibility and usability of GMF, we have developed a web application with a metabolic network database to predict a flux distribution of genetically modified mutants. One hundred and twelve data sets of Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Chinese hamster ovary were registered as standard models.





  • Metabolic analysis of antibody producing Chinese hamster ovary cell culture under different stresses conditions
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Md. Bahadur Badsha, Hiroyuki Kurata, Masayoshi Onitsuka, Takushi Oga, Takeshi Omasa

    Chinese hamster ovary (CHO) cells are commonly used as the host cell lines concerning their ability to produce therapeutic proteins with complex post-translational modifications. In this study, we have investigated the time course extra- and intracellular metabolome data of the CHO–K1 cell line, under a control and stress conditions. The addition of NaCl and trehalose greatly suppressed cell growth, where the maximum viable cell density of NaCl and trehalose cultures were 2.2-fold and 2.8-fold less than that of a control culture. Contrariwise, the antibody production of both the NaCl and trehalose cultures was sustained for a longer time to surpass that of the control culture. The NaCl and trehalose cultures showed relatively similar dynamics of cell growth, antibody production, and substrate/product concentrations, while they indicated different dynamics from the control culture. The principal component analysis of extra- and intracellular metabolome dynamics indicated that their dynamic behaviors were consistent with biological functions. The qualitative pattern matching classification and hierarchical clustering analyses for the intracellular metabolome identified the metabolite clusters whose dynamic behaviors depend on NaCl and trehalose. The volcano plot revealed several reporter metabolites whose dynamics greatly change between in the NaCl and trehalose cultures. The elastic net identified some critical, intracellular metabolites that are distinct between the NaCl and trehalose. While a relatively small number of intracellular metabolites related to the cell growth, glucose, glutamine, lactate and ammonium ion concentrations, the mechanism of antibody production was suggested to be very complicated or not to be explained by elastic net regression analysis.





  • Preparation of Quenchbodies by protein transamination reaction
    Publication date: July 2016
    Source:Journal of Bioscience and Bioengineering, Volume 122, Issue 1

    Author(s): Jinhua Dong, Hee-Jin Jeong, Hiroshi Ueda

    Quenchbody (Q-body) is an antibody fragment labeled with fluorescent dye(s), which functions as a biosensor via the antigen-dependent removal of the quenching effect on fluorophores. It is based on the principle that the fluorescence of the dye(s) attached to the antibody N-terminal region is quenched primarily by the tryptophan residues present in the variable regions, and this quenching is released when the antigen binds to the antibody, resulting in increased fluorescence intensity. Hence Q-body is utilized in various immunoassays for the rapid and sensitive detection of analytes. So far, Q-bodies have been prepared by using a cell-free translation system or by combining Escherichia coli expression and post-labeling steps. However, the above methods need antibody gene cloning, and are time-consuming. In this study, we report a novel approach to prepare Q-bodies by protein N-terminal transamination. We used the antigen-binding fragment (Fab) of an antibody against the bone-Gla-protein (BGP), a biomarker for bone diseases, which was expressed in E. coli. The purified Fab was treated with Rapoport's salt to convert the amino group at the N-terminus to a ketone group, which in turn was allowed to react with fluorescent probes that have aminooxy or hydrazide groups, to prepare a Q-body. The Q-body prepared by this method could detect the BGP-C7 antigen at concentrations as low as 10 nM. Since the approach can label the protein N-terminus directly, it could be applied for preparing Q-bodies from natural antibodies and for the rapid screening of high-performance Q-bodies.