• KSBB Journal
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• v.16 no.3
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• pp.290-294
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• 2001

The removal of nitrogen compounds from waste water is essential and is often accomplished by biological process. The denitrifying bacterium, Paracoccus denitrificans (KCTC 2530), was employed to study the characteristics and the denitrification differences of Permeabilized strains and untreated strains. The permeabilization rate increased with increasing toluene concentration, but some part of the toluene contributed to denaturing the datachment of proteins from the plasma membrane. Permeabilized Paracoccus denitrificans had long lag phase and high specific growth rate in cultivation, and showed excellent denitrification characteristic compared with untreated strains. But, in both cases, the denitrification ability was significantly reduced after 4 or 5 denitrifications. It seems that the strains fall into the death phase when the nutrient was exhausted. When the nutrient recovered to its initial level, the denitrification ability also recovered to the normal level. The results obtained were encouraging enough to apply to practical water treatment situation.

• Journal of Microbiology and Biotechnology
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• v.7 no.6
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• pp.391-396
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• 1997

Two series of carbon sources, linear primary $C_1$~$C_9$ alcohols and linear $C_2$~$C_{10}$ monocarboxylic acids were tested for PHA synthesis in Paracoccus denitrificans. The results showed that the growth-associated synthesis of PHA could be referred only to the carbon sources with odd number of carbon except methanol. For all carbon sources with even number of carbon, nitrogen limitation was required to induce PHA synthesis in P. denitrificans. Poly(3-hydroxyvalerate)[P(3HV)] homopolymer was synthesized from $C_5$, $C_7$, and $C_9$ while growing in the presence of nitrogen, but the nitrogen depletion in the later growth period incorporated 3-hydroxybutyrate(3HB) unit into the polymer chain. The optimum C/N ratio for P(3HV) homopolymer production was found to be 10 when the strain was grown on 10 ml/l of valeric acid for 96 h. P. denitrificans synthesized P(3HB-co-3HV) copolymers from n-hexanoic and n-octanoic acid. The microstructural characterics of the P(3HB-co-3HV) copolymer from n-propanol was investigated using $^13C$-nuclear magnetic resonance spectroscopy, showing a structural heterogeneity.

• Journal of Microbiology and Biotechnology
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• v.34 no.9
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• pp.1826-1835
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• 2024

Paracoccus denitrificans has been identified as a representative strain with heterotrophic nitrificationaerobic denitrification capabilities (HN-AD), and demonstrates strong denitrification proficiency. Previously, we isolated the DYTN-1 strain from activated sludge, and it has showcased remarkable nitrogen removal abilities and genetic editability, which positions P. denitrificans DYTN-1 as a promising chassis cell for synthetic biology engineering, with versatile pollutant degradation capabilities. However, the strain's low stability in plasmid conjugation transfer efficiency (PCTE) hampers gene editing efficacy, and is attributed to its restriction modification system (R-M system). To overcome this limitation, we characterized the R-M system in P. denitrificans DYTN-1 and identified a DNA endonuclease and 13 DNA methylases, with the DNA endonuclease identified as HNH endonuclease. Subsequently, we developed a plasmid artificial modification approach to enhance conjugation transfer efficiency, which resulted in a remarkable 44-fold improvement in single colony production. This was accompanied by an increase in the frequency of positive colonies from 33.3% to 100%. Simultaneously, we cloned, expressed, and characterized the speculative HNH endonuclease capable of degrading unmethylated DNA at 30℃ without specific cutting site preference. Notably, the impact of DNA methylase M9 modification on the plasmid was discovered, significantly impeding the cutting efficiency of the HNH endonuclease. This revelation unveils a novel R-M system in P. denitrificans and sheds light on protective mechanisms employed against exogenous DNA invasion. These findings pave the way for future engineering endeavors aimed at enhancing the DNA editability of P. denitrificans.

• KSBB Journal
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• v.20 no.2 s.91
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• pp.100-105
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• 2005

Removal of nitrogen compound from waste water is essential and often accomplished by biological process. Denitrification bacterium, Paracoccus denitrificans (KCTC 2350) is employed to estimate the denitrification ability and the characteristics. In the immobilized biological reactor system, the measurement of absolute amount of active strain in the reactor is comparatively difficult or impossible. In this. study, a reactor was designed with the unwoven texture wrapped peep holed plastic tube to calculate the absolute amount of active strain by comparing the activity of the permeabilized and or immobilized reactor and the free cell reactor The reactor system was continuous stirred tank reactor and the reaction rate of substrate consumption was assumed to satisfy the Michaelis-Menten equation. The effluent concentration of nitrate and nitrite was measured to estimate the apparent parameter of Michaelis-Menten equation. As a result, we found that the amount of immobilized active strain was figured out to be half of the total active strain in the reactor and the time required to be reached in the equilibrium state in the permeabilized and or immobilized reactor system was figured out to be shorter than that of the free cell reactor system.

• Journal of Microbiology and Biotechnology
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• v.27 no.6
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• pp.1106-1111
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• 2017

Escherichia coli was engineered to sense methanol by employing a chimeric two-component system (TCS) strategy. A chimeric MxaY/EnvZ (MxaYZ) TCS was constructed by fusing the Paracoccus denitrificans MxaY with the E. coli EnvZ. Real-time quantitative PCR analysis and GFP-based fluorescence analysis showed maximum transcription of ompC and the fluorescence at 0.01% of methanol, respectively. These results suggested that E. coli was successfully engineered to sense methanol by the introduction of chimeric MxaYZ. By using this strategy, various chimeric TCS-based bacterial biosensors can be constructed and used for the development of biochemical-producing recombinant microorganisms.

• Journal of Life Science
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• v.11 no.3
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• pp.273-278
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• 2001

Removal of nitrogen compound from waste water is essential and often accomplished by biological process. Deni-trification bacterium. Paracoccus denitrificans(KCTC 2350) is employed to estimate the ability and the characteristics of denitrification. In the immobilized biological reactor system, the measurement of absolute amount of active strain in the reactor is comparatively difficult or impossible. In this study, strain immobilized denitrification reactor was designed with the unwoven texture wrapped peeped hole plastic tube to calculated the absolute amount of active strain by comparing the activity of the immobilized reactor adn the free cell reactor. The reactor system was continuous stirred tank reactor and the rate of substrate consumption was assumed to be Michaelis-Menten equation. As a result, we found that the amount of immobilized active strain was the half of the total active strain in the reactor and the time required to reach in the equilibrium state in the immobilized reactor system was shorter than that of the free cell reactor system.

• Korean Journal of Microbiology
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• v.46 no.1
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• pp.46-51
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• 2010

Coenzyme Q10 (CoQ10) is an essential lipid-soluble component of membrane-bound electron transport chains. CoQ10 is involved in several aspects of cellular metabolism and is increasingly being used in therapeutic applications for several diseases. Despite the recent accomplishments in metabolic engineering of Escherichia coli for CoQ10 production, the production levels are not yet competitive with those by fermentation or isolation. So we tested several microorganisms obtained from the KCTC of Biological Resource Center to find novel sources of strain-development for CoQ10-production. Then we selected two strains, Paracoccus denitrificans (KCTC 2530) and Asaia siamensis (KCTC 12914), and tested to optimize the CoQ10 production conditions. Among the carbon sources tested, CoQ10 production was the highest when fructose was supplied about 4% concentration. Yeast extract produced the highest CoQ10 production about 2% concentration. The highest CoQ10 production was obtained at pH 6.0 for P. denitrificans and pH 8.0 for A. siamensis. And two strains showed the highest CoQ10 production at $30^{\circ}C$, but the highest DCW was obtained at $37^{\circ}C$. In the fed-batch culture, P. denitrificans yielded $14.34{\pm}0.473$ mg and A. siamensis yielded $12.53{\pm}0.231$ mg of final CoQ10 production.

• Korean Journal of Food Science and Technology
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• v.30 no.4
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• pp.902-907
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• 1998

In this study the anaerobic degradation of nitrate by in GFM (gel and foam matrix) and bead gel immobilized Paracoccus denitrificans DSM 65 in continous culture was conducted. A novel GFM immobilization system was developed in order to improve conventional system (bead). With increasing nitrate concentration in water, the nitrate reduction rate was increased. The observed maximum denitrification rate by in GFM immobilized cells was 177 mg/L h in buffered water, while that was 33 mg/L h in tap water. In comparison with bead system the reduction activity by GFM system showed $1.2{\sim}2.1$ times better. The denitrification activity was not changed after 16 days storage at $5^{\circ}C$ and also showed better activity than that of free cells or even bead immobilized cells.

• Korean Journal of Soil Science and Fertilizer
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• v.39 no.6
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• pp.409-414
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• 2006

Sulfur-oxidizing bacteria were enumerated and isolated from a steady-state anaerobic master culture reactor (MCR) operated for over six months under a semi-continuous mode and nitrate-limiting conditions using thiosulfate as an electron donor. Most are Gram-negative bacteria, which have sizes up to 12 m. Strains AD1 and AD2 were isolated from the plate count agar (PCA), and strains BD1 and BD2 from the solid thiosulfate/nitrate medium. Based on the morphological, physiological, FAME and 16S rDNA sequence analyses, the two dominant strains, AD1 and AD2, were identified as Paracoccus denitrificans and Paracoccus versutus (formerly Thiobacillus versutus), respectively. From the physiological results, glucose was assimilated by both strains AD1 and AD2. Heterotrophic growth of strains AD1 and AD2 could be a more efficient way of obtaining a greater amount of biomass for use as an inoculum. Even though facultative autotrophic bacteria grow under heterotrophic conditions, autotrophic denitrification would not be reduced.

• Journal of Microbiology and Biotechnology
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• v.31 no.8
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• pp.1154-1162
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• 2021

The transcriptional capacities of target genes are strongly influenced by promoters, whereas few studies have focused on the development of robust, high-performance and cross-species promoters for wide application in different bacteria. In this work, four novel promoters (P_k.rtufB, P_k.r1, P_k.r2, and P_k.r3) were predicted from Ketogulonicigenium robustum and their inconsistency in the -10 and -35 region nucleotide sequences indicated they were different promoters. Their activities were evaluated by using green fluorescent protein (gfp) as a reporter in different species of bacteria, including K. vulgare SPU B805, Pseudomonas putida KT2440, Paracoccus denitrificans PD1222, Bacillus licheniformis and Raoultella ornithinolytica, due to their importance in metabolic engineering. Our results showed that the four promoters had different activities, with P_k.r1 showing the strongest activity in almost all of the experimental bacteria. By comparison with the commonly used promoters of E. coli (tufB, lac, lacUV5), K. vulgare (Psdh, Psndh) and P. putida KT2440 (JE111411), the four promoters showed significant differences due to only 12.62% nucleotide similarities, and relatively higher ability in regulating target gene expression. Further validation experiments confirmed their ability in initiating the target minCD cassette because of the shape changes under the promoter regulation. The overexpression of sorbose dehydrogenase and cytochrome c551 by P_k.r1 and P_k.r2 resulted in a 22.75% enhancement of 2-KGA yield, indicating their potential for practical application in metabolic engineering. This study demonstrates an example of applying bioinformatics to find new biological components for gene operation and provides four novel promoters with broad suitability, which enriches the usable range of promoters to realize accurate regulation in different genetic backgrounds.