• Journal of Microbiology and Biotechnology
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• v.19 no.9
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• pp.911-917
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• 2009

The apoptotic caspases have been classified in accordance with their substrate specificities, as the optimal tetrapeptide recognition motifs for a variety of caspases have been determined via positional scanning substrate combinatorial library technology. Here, we focused on two proteolytic recognition motifs, DEVD and IETD, owing to their extensive use in cell death assay. Although DEVE and IETD have been generally considered to be selective for caspase-3 and -8, respectively, the proteolytic cleavage of these substrates does not display absolute specificity for a particular caspase. Thus, we attempted to monitor the cleavage preference for caspase-3, particularly using the recombinant protein substrates. For this aim, the chimeric GST:DEVD:EGFP and GST:IETD:EGFP proteins were genetically constructed by linking GST and EGFP with the linkers harboring DEVD and IETD. To our best knowledge, this work constitutes the first application for the monitoring of cleavage preference employing the recombinant protein substrates that simultaneously allow for mass and fluorescence analyses. Consequently, GST:IETD:EGFP was cleaved partially in response to caspase-3, whereas GST:DEVD:EGFP was completely proteolyzed, indicating that GST:DEVD:EGFP is a better substrate than GST:IETD:EGFP for caspase-3. Collectively, using these chimeric protein substrates, we have successfully evaluated the feasibility of the recombinant protein substrate for applicability to the monitoring of cleavage preference for caspase-3.

• The Korean Journal of Malacology
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• v.32 no.1
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• pp.31-36
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• 2016

In the present study, we observed a unique association of the flat oyster, Ostrea denselamellosa obtained from a muddy substrate at Haechang Bay, the south coast of Korea in the spring of 2013. Fossilized or semi-fossilized veneriid clam shells, possibly Ruditapes philippinarum, were found adhering to the umbonal area of the flat oyster valves. This unique association of the flat oyster shells with the fossilized clam shells suggested that the flat oyster larvae utilized the clam shells as substrate during settlement. Since availability of clam shells in the muddy subtidal environment is limited, this unique substrata for the flat oyster larvae may limit recruitment of the flat oysters in the bay.

• Journal of Microbiology and Biotechnology
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• v.33 no.2
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• pp.268-276
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• 2023

Alkyl butyrate with fruity flavor is known as an important additive in the food industry. We synthesized various alkyl butyrates from various fatty alcohol and butyric acid using immobilized Rhodococcus cutinase (Rcut). Esterification reaction was performed in a non-aqueous system including heptane, isooctane, hexane, and cyclohexane. As a result of performing the alkyl butyrate synthesis reaction using alcohols of various chain lengths, it was found that the preference for the alcohol substrate had the following order: C6 > C4 > C8 > C10 > C2. Through molecular docking analysis, it was found that the greater the hydrophobicity of alcohol, the higher the accessibility to the active site of the enzyme. However, since the number of torsions increased as the chain length increased, it became difficult for the hydroxyl oxygen of the alcohol to access the ^γO of serine at the enzyme active site. These molecular docking results were consistent with substrate preference results of the Rcut enzyme. The Rcut maintained the synthesis efficiency at least for 5 days in isooctane solvent. We synthesized as much as 452 mM butyl butyrate by adding 100 mM substrate daily for 5 days and performing the reaction. These results show that Rcut is an efficient enzyme for producing alkyl butyrate used in the food industry.

• Journal of Microbiology
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• v.37 no.4
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• pp.224-228
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• 1999

Benzaldehyde dehydrogenase (BZDH), an enzyme involved in the degradation of toluene and xylenes, is encoded by the phnN gene of Pseudomonas sp. strain DJ77. We determined the nucleotide sequence of a DNA fragment of 1,803 base pairs which included the phnN gene. The fragment contained an open reading frame of 1,506 base pairs to accommodate th 55 kDa sized enzyme encoding BZDH. The enzyme efficiently oxidized benzaldehyde, salicylaldehyde, m-tolualdehyde and ps-tolualdehyde.

• Microbiology and Biotechnology Letters
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• v.24 no.4
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• pp.385-392
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• 1996

Bacillus stearotheymophilus, a potent xylanolytic bacterium isolated from soil, was tested for the strain's strategies of pentose utilization and the evidence of substrate preferences. The strain metabolized glucose, xylose, ribose, maltose, cellobiose, sucrose, arabinose and xylitol. The efficacy of the sugars as a carbon and energy source in this strain was of the order named above. The organism, however, could not grow on glycerol as a sole growth substrate. During cultivation on a mixture of glucose and xylose or arabinose, the major hydrolytic products of xylan, B. stearothermophilus displayed classical diauxic growth in which glucose was utilized during the first phase. On the other hand, the pentose utilization was prevented immediately upon addition of glucose. Cellobiose was preferred over xylose or arabinose. In contrast, maltose and pentose were co-utilized, and also no preference on between xylose and arabinose. Enzymatic studies indicated that B. stearothermophilus possessed constitutive hexokinase, a key enzyme of the glucose metabolic system. While, the production of $^{D}$-xylose isomerase, $^{D}$-xylulokinase and $^{D}$-arabinose isomerase essential for pentose phosphate pathway were induced by xylose, xylan, and xylitol but repressed by glucose. Taken together, the results suggested that the sequential utilization of B. stearothermophilus would be mediated by catabolite regulatory mechanisms such as catabolite inhibition or inducer exclusion.

• Korean Journal of Ecology and Environment
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• v.50 no.3
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• pp.355-361
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• 2017

In this study, we investigated the response of freshwater oligochaete, Tubifex tubifex, to the water temperature changes and the differences of substrate composition in a laboratory condition. The changes of body shape were observed in a test cage according to the water temperature change ranging from $10^{\circ}C$ to $30^{\circ}C$ with $2^{\circ}C$ interval every 10 minutes. The substrate preference was observed with four different substrate composition from silt-clay to coarse sand. Our results displayed that T. tubifex preferred substrates with the smallest particle size (<0.063 mm). The water temperature influenced on the activity and body shape of T. tubifex, showing low activity with the coiled and constricted body shapes at lower temperature and high activity with relaxed linear body shapes at higher temperature.

• Journal of Magnetics
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• v.21 no.2
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• pp.168-172
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• 2016

$BiMnO_3$ has been a promising candidate as a magnetoelectric multiferroic while there have been many controversial reports on its ferroelectricity. The detailed analysis of its film growth, especially the growth of thin film having monoclinic symmetry has not been reported. We studied the effect of miscut angle, the substrate surface, and film thickness on the symmetry of $BiMnO_3$ thin film. A flat $SrTiO_3$ (110) substrate resulted in a thin film with three domains of $BiMnO_3$ and 1 degree miscut in the $SrTiO_3$ (110) substrate resulted in dominant domain preference in the $BiMnO_3$ thin film. The larger miscut resulted in a nearly perfect detwinned $BiMnO_3$ film with a monoclinic phase. This strong power of domain selection due to the step edge of the substrate was efficient even for the thicker film which showed a rather relaxed growth behavior along the $SrTiO_3$ [1-10] direction.

• Journal of Microbiology and Biotechnology
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• v.32 no.7
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• pp.949-954
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• 2022

The lipolytic yeast Candida aaseri SH14 contains three Acyl-CoA oxidases (ACOXs) which are encoded by the CaAOX2, CaAOX4, and CaAOX5 genes and catalyze the first reaction in the β-oxidation of fatty acids. Here, the respective functions of the three CaAOX isozymes were studied by growth analysis of mutant strains constructed by a combination of three CaAOX mutations in minimal medium containing fatty acid as the sole carbon source. Substrate specificity of the CaAOX isozymes was analyzed using recombinant C. aaseri SH14 strains overexpressing the respective genes. CaAOX2 isozyme showed substrate specificity toward short- and medium-chain fatty acids (C6-C12), while CaAOX5 isozyme preferred long-chain fatty acid longer than C12. CaAOX4 isozyme revealed a preference for a broad substrate spectrum from C6-C16. Although the substrate specificity of CaAOX2 and CaAOX5 covers medium- and long-chain fatty acids, these two isozymes were insufficient for complete β-oxidation of long-chain fatty acids, and therefore CaAOX4 was indispensable.

• BMB Reports
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• v.32 no.4
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• pp.399-404
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• 1999

2,3-Dihydroxybiphenyl 1,2-dioxygenase (2,3-DHBD), which catalyzes the ring meta-cleavage of 2,3-dihydroxybiphenyl, is encoded by the phnQ gene of biphenyl- and phenanthrene-degrading Pseudomonas sp. strain DJ77. We determined the nucleotide sequence of a DNA fragment of 1497 base pairs which included the phnQ gene. The fragment lncluded an open reading frame of 903 base pairs to accommodate the enzyme. The predicted amino acid sequence of the enzyme subunit consisted of 300 residues. In front of the gene, a sequence resembling an E. coli promoter was identified, which led to constitutive expression of the cloned gene in E. coli. The deduced amino acid sequence of the PhnQ enzyme exhibited 85.6% identity with that of the corresponding enzyme in Sphingomonas yanoikuyae Q1 (formerly S. paucimobilis Q1) and 22.1% identity with that of catechol 1,2,3-dioxygenase from the same DJ77 strain. PhnQ showed broader substrate preference than previously-cloned PhnE, catechol 2,3-dioxygenase. Ten amino acid residues, considered to be important for the role of extradiol dioxygenases, were conserved.

• Mycobiology
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• v.50 no.5
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• pp.326-344
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• 2022

The fungal-like family Saprolegniaceae (Oomycota), also called "water mold," includes mostly aquatic saprophytes as well as notorious aquatic animal pathogens. Most studies on Saprolegniaceae have been biased toward pathogenic species that are important to aquaculture rather than saprotrophic species, despite the latter's crucial roles in carbon cycling of freshwater ecosystems. Few attempts have been made to study the diversity and ecology of Saprolegniaceae; thus, their ecological role is not well-known. During a survey of oomycetes between 2016 and 2021, we investigated the diversity and distribution of culturable Saprolegniaceae species in freshwater ecosystems of Korea. In the present study, members of Saprolegniaceae were isolated and identified at species level based on their cultural, morphological, and molecular phylogenetic analyses. Furthermore, substrate preference and seasonal dynamics for each were examined. Most of the species were previously reported as animal pathogens; however, in the present study, they were often isolated from other freshwater substrates, such as plant debris, algae, water, and soil sediment. The relative abundance of Saprolegniaceae was higher in the cold to cool season than that in the warm to hot season of Korea. This study enhances our understanding of the diversity and ecological attributes of Saprolegniaceae in freshwater ecosystems.