• Journal of Microbiology and Biotechnology
• /
• v.22 no.4
• /
• pp.470-478
• /
• 2012

Recent genome comparisons of E. coli B and K-12 strains have indicated that the makeup of the cell envelopes in these two strains is quite different. Therefore, we analyzed and compared the envelope proteomes of E. coli BL21(DE3) and MG1655. A total of 165 protein spots, including 62 nonredundant proteins, were unambiguously identified by two-dimensional gel electrophoresis and mass spectrometry. Of these, 43 proteins were conserved between the two strains, whereas 4 and 16 strain-specific proteins were identified only in E. coli BL21(DE3) and MG1655, respectively. Additionally, 24 proteins showed more than 2-fold differences in intensities between the B and K-12 strains. The reference envelope proteome maps showed that E. coli envelope mainly contained channel proteins and lipoproteins. Interesting proteomic observations between the two strains were as follows: (i) B produced more OmpF porin with a larger pore size than K-12, indicating an increase in the membrane permeability; (ii) B produced higher amounts of lipoproteins, which facilitates the assembly of outer membrane ${\beta}$-barrel proteins; and (iii) motility- (FliC) and chemotaxis-related proteins (CheA and CheW) were detected only in K-12, which showed that E. coli B is restricted with regard to migration under unfavorable conditions. These differences may influence the permeability and integrity of the cell envelope, showing that E. coli B may be more susceptible than K-12 to certain stress conditions. Thus, these findings suggest that E. coli K-12 and its derivatives will be more favorable strains in certain biotechnological applications, such as cell surface display or membrane engineering studies.

• Journal of Microbiology and Biotechnology
• /
• v.18 no.4
• /
• pp.778-783
• /
• 2008

Anthrax is an infectious disease caused by toxigenic strains of the Gram-positive bacterium Bacillus anthracis. To identify the mitochondrial proteins that are expressed differently in murine macrophages infected with spores of B. anthracis Sterne, proteomic and MALDI-TOF/MS analyses of uninfected and infected macrophages were conducted. As a result, 13 mitochondrial proteins with different expression patterns were discovered in the infected murine macrophages, and some were identified as ATP5b, NIAP-5, ras-related GTP binding protein B isoform CRAa, along with several unnamed proteins. Among these proteins, ATP5b is related to energy production and cytoskeletal rearrangement, whereas NIAP-5 causes apoptosis of host cells due to binding with caspase-9. Therefore, this paper focused on ATP5b, which was found to be down regulated following infection. The downregulated ATP5b also reduced ATP production in the murine macrophages infected with B. anthracis spores. Consequently, this study represents the first mitochondrial proteome analysis of infected macrophages.

• Journal of Microbiology and Biotechnology
• /
• v.20 no.1
• /
• pp.138-145
• /
• 2010

A bacterial strain isolated from soil for its potential to control the anthracnose disease caused by Colletotrichum gloeosporioides was identified as a Bacillus subtilis. Bacillus subtilis CMB32 produced antifungal agents on M9 broth at $30^{\circ}C$. Biosurfactant lipopeptides produced by Bacillus subtilis CMB32 were precipitated by adjusting to pH 2 and extracting using chloroform/methanol, and then were purified using column chromatography and reverse-phase HPLC. The molecular masses of the lipopeptides were estimated by MALDI-TOF mass spectrometry as (a) 1,080, (b) 1,486, and (c) 1,044 Da, respectively. They had cyclic structures and amino acid compositions of (a) Pro, Asx, Ser, Tyr, Glx, (b) Glx, Tyr, Thr, Ala, Pro, lie, and (c) Glx, Leu, Val, Asx, respectively. Further analysis revealed that Bacillus subtilis CMB32 produced three antifungal lipopeptides: (a) iturin A, (b) fengycin, and (c) surfactin A.

• Asian Pacific Journal of Cancer Prevention
• /
• v.13 no.6
• /
• pp.2711-2715
• /
• 2012

Background: Bisphenol A (BPA), an endocrine disrupting chemical, has been suspected to pose carcinogenic risks. However, likely mechanisms are obscure and there are difficulties to estimating its real significance for cancer development. Methods: We therefore studied BPA-induced proteomic alterations in immune organs of ICR mice offspring that were prenatally exposed to BPA (15 and 300 mg/L of drinking water). We performed 2D-gel analyses of samples, considering differences in spleen, exposure levels, sex, and ages. Results: From proteomic analyses, we found various proteins were up- or down-regulated by BPA. Among them, SET, a putative oncogene and inhibitor of phosphatase 2A, was significantly down-regulated in a BPA dose-dependent manner. We also confirmed down-regulation of SET in western blot and real time PCR analyses. From gene network analysis, SET is predicted to communicate with other genes including CYP17, which is involved in biosynthesis and metabolism of sex-hormones. Conclusions: This study provided evidence that SET can be applied as a new biomarker for prenatal BPA exposure and suggests a potential new mechanism of action in that BPA may disrupt CYP17 via SET.

• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2000.11a
• /
• pp.32-34
• /
• 2000

Computational chemistry is a discipline using computational methods for the calculation of molecular structure, properties, and reaction or for the simulation of molecular behavior. Relating and turning the complexity of data from genomics, high-throughput screening, combinatorial chemical synthesis, gene-expression investigations, pharmacogenomics, and proteomics into useful information and knowledge is the primary goal of bioinformatics. In particular, the structure-based molecular design is one of essential fields in bioinformatics and it can be called as structural bioinformatics. Therefore, the conformational analysis for proteins and peptides using the techniques of computational chemistry is expected to play a role in structural bioinformatics. There are two major computational methods for conformational analysis of proteins and peptides; one is the molecular orbital (MO) method and the other is the force field (or empirical potential function) method. The MO method can be classified into ab initio and semiempirical methods, which have been applied to relatively small and large molecules, respectively. However, the improvement in computer hardwares and softwares enables us to use the ab initio MO method for relatively larger biomolecules with up to v100 atoms or ∼800 basis functions. In order to show how computational chemistry can be used in structural bioinformatics, 1 will present on (1) cis-trans isomerization of proline dipeptide and its derivatives, (2) positional preference of proline in ${\alpha}$-helices, and (3) conformations and activities of Arg-Gly-Asp-containing tetrapeptides.

• Journal of Microbiology and Biotechnology
• /
• v.27 no.11
• /
• pp.2028-2036
• /
• 2017

The Escherichia coli K-12 and B strains are among the most frequently used bacterial hosts for scientific research and biotechnological applications. However, omics analyses have revealed that E. coli K-12 and B exhibit notably different genotypic and phenotypic attributes, even though they were derived from the same ancestor. In a previous study, we identified a limited number of proteins from the two strains using two-dimensional gel electrophoresis and tandem mass spectrometry (MS/MS). In this study, an in-depth analysis of the physiological behavior of the E. coli K-12 and B strains at the proteomic level was performed using six-plex isobaric tandem mass tag-based quantitative MS. Additionally, the best lysis buffer for increasing the efficiency of protein extraction was selected from three tested buffers prior to the quantitative proteomic analysis. This study identifies the largest number of proteins in the two E. coli strains reported to date and is the first to show the dynamics of these proteins. Notable differences in proteins associated with key cellular properties, including some metabolic pathways, the biosynthesis and degradation of amino acids, membrane integrity, cellular tolerance, and motility, were found between the two representative strains. Compared with previous studies, these proteomic results provide a more holistic view of the overall state of E. coli cells based on a single proteomic study and reveal significant insights into why the two strains show distinct phenotypes. Additionally, the resulting data provide in-depth information that will help fine-tune processes in the future.

• Mass Spectrometry Letters
• /
• v.12 no.4
• /
• pp.126-130
• /
• 2021

The mass spectrometry (MS) provides the mass-to-charge ratios of atoms, molecules, stable/metastable complexes, and their fragments. I have taken a long journey with MS to address outstanding issues and problems by experiments and theory and gain insights into underlying principles in chemistry. By looking through the mass-to-charge ratio, I have studied thermochemical problems in silicon chemistry, the infrared multiphoton dissociation spectroscopy of organometallic intermediates, unimolecular dissociations of halotoluene radical cations, and the kinetics of association/dissociation of alkali halide triple ions with Lewis bases. Various MS platforms have been used to characterize non-covalent interactions between porphyrins and fullerenes and those between the group IIB ions and trioctylchalcogenides, and to examine the binding of the group IA, IIA and porphyrin ions to G-quadruplex DNA. Recently, I have focused on mass-balanced H/D isotope dipeptide tags for MS-based quantitative proteomics, a simple chemical modification method for MS-based lipase assay, and the kinetics and dynamics of energy-variable collision-induced dissociation of chemically modified peptides. Now, I see an important role of MS in global issues in the post-COVID era, as the society demands high standards for indoor air quality to contain the airborne-pathogen transmission as well as in-situ monitoring and tracking of carbon emissions to reduce global warming.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.4
• /
• pp.917-923
• /
• 2009

The maize lipoxgyenase-1 is a non-traditional dual positional specific enzyme and the reaction proceeds via enzyme-initiated catalysis. Bioinformatic analysis indicated that the maize lipoxygenase-1 is structurally more similar to soybean LOX1 than pea LOXN2 in that it has an additional external loop (residues 318-351) in the carboxy-terminal catalytic domain. We analyzed the dependence of product distribution on concentration of linoleic acid and monitored the formation of hydroperoxyoctadecadienoic acid as a function of enzyme concentration. Product distribution was strongly influenced by substrate concentration, such that kinetically-controlled regioisomers were enriched and thermodynamically-controlled regioisomers were depleted at high substrate concentration. Kinetic studies indicated that the formation of hydroperoxyoctadecadienoic acid saturated rapidly in an enzyme concentration-dependent manner, which implied that reactivation by reoxidation of inactive Fe(II) failed to occur. Our results support the previously proposed enzyme-initiated catalytic mechanism of the maize lipoxgyenase-1 and reveals that a substrate molecule serves as a hydrogen atom donor in its enzyme-initiated catalysis.

• Fisheries and Aquatic Sciences
• /
• v.25 no.7
• /
• pp.390-402
• /
• 2022

In this study we investigate physical and chemical characteristics of immature and mature skipjack tuna (Katsuwonus pelamis) roes in fresh and dried forms. Fresh roes were studied for histological structure and also dried by three methods: hot air drying (HD), vacuum drying (VD) and freeze drying (FD). The obtained roe powders were analysed for proximate composition, color value, fatty acid composition, amino acid profile, equivalent umami concentration (EUC) and protein pattern. Unyolked oocytes were more common in immature roes, while fully yolked oocytes were more common in mature roes. All dried tuna roes contained high content of protein and lipid (69.31%-70.55% and 11.14%-16.02%, respectively). The powders obtained by FD provided the highest lightness value (L^*). The main fatty acid found in all roe powders was docosahexaenoic acid (DHA) (23.49%-27.02%). Glutamic acid, leucine, and aspartic acid were the three most abundant amino acids found in the powders (13.58-14.61, 8.06-8.42, and 7.81-8.39 g/100 g of protein, respectively). The mature roe powder obtained from HD provided the highest EUC value (73.09 g monosodium glutamate/100 g of samples). The protein band at molecular weight of 97 kDa (vitelline) represented the major protein. Therefore, dried tuna roe could be a functional ingredient source of protein and lipid rich in DHA and it also has potential to be used as taste enhancer with umami compound.

• Applied Chemistry for Engineering
• /
• v.34 no.6
• /
• pp.649-659
• /
• 2023

This study was initiated to evaluate the phosphorus (P) removal and diesel oil degradation by bacteria isolated from industrial wastewater. The bacteria isolated were identified as Bacillus sp. The P removal efficiencies by Bacillus sp. were 99% at the initial 20 mg/L P concentration. The diesel degradation efficiencies by Bacillus sp. were 86.4% at an initial 1% diesel concentration. Lipophilicity by bacteria was the highest in the log phase, whereas it was the lowest in the death phase. As the diesel was used as a carbon source, P removal efficiencies by Bacillus sp. were 68%. When glucose, acetate, and a mixture of glucose and acetate as second carbon sources were added, the diesel degradation efficiencies were 69.22%, 65.46%, and 51.46%, respectively. The diesel degradation efficiency was higher in the individual additions of glucose or acetate than in the mixture of glucose and acetate. When P concentration increased from 20 mg/L to 30 mg/L, the diesel degradation efficiency was increased by 7% from 65% to 72%, whereas when P concentration was increased from 30 mg/L to 40 mg/L, there was no increase in diesel degradation. One of the five proteins identified by proteome analysis in the 0.5% diesel-treated samples may be involved in alkane degradation and is known as the cytochrome P450 system. Also, two of the sixteen proteins identified in the 1.5% diesel-treated samples may be implicated in the fatty acid transport system and alcohol dehydrogenation.