- Monitoring 4-Chlorobiphenyl-Degrading Bacteria in Soil Microcosms by Competitive Quantitative PCR
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Soo Youn Lee , Min Sup Song , Kyung Man You , Bae Hoon Kim , Seong Ho Bang , In Soo Lee , Chi Kyung Kim , Yong Keun Park
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J. Microbiol. 2002;40(4):274-281.
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 Abstract
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The competitive quantitative PCR method targeting pcbC gene was developed for monitoring 4-chlorobiphenyl(4CB)-degrading bacteria, Pseudomonas sp. strain DJ-12, in soil microcosms. The method involves extraction of DNA from soil contaminated with 4CB, PCR amplification of a pcbC gene fragment from the introduced strain with a set of strain-specific primers, and quantification of the electrophoresed PCR product by densitometry. To test the adequacy of the method, Pseudomonas sp. Strain DJ-12 was introduced into both contaminated and non-contaminated soil microcosms amended with 4CB. Pseudomonas sp. strain DJ-12 was monitored and quantified by a competitive quantitative PCR in comparison with 4CB degradation and the result was compared to those obtained by using the conventional cultivation method. We successfully detected and monitored 4CB-degrading bacteria in each microcosm and found a significant linear relationship between the number of 4CB-degrading bacteria and the capacity for 4CB biodegradation. The results of DNA spiking and cell-spreading experiments suggest that this competitive quantitative PCR method targeting the pcbC gene for monitoring 4Cbdegrading bacteria appears to be rapid, sensitive and more suitable than the microbiological approach in estimating the capacity of 4CB biodegradation in environmental samples.
- Cloning and Sequencing Analysis of cadC Encoding Transcriptional Activator CadC from Salmonella typhimurium
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Bae Hoon Kim , Ho Jeong Lee , In Soo Lee , Sung Ho Bang
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J. Microbiol. 2001;39(2):109-115.
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Abstract
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Salmonella typhimurium possesses a cad operon, which contributes to an adaptive response against an acidifying environment. In Escherichia coli, the activation of the cad operon is dependent on cadC, which is located upstream of the operon. However, the activator of cad operon in S. typhimurium has not been known until now. In this study, we selected a putative cadC mutant by trasposon mutagenesis and cloned the cadC of S. typhimurium. Moreover, the cadC mutant was complemented by cadC clone. The cadC gene from S. typhimurium LT-2 consists of 1539 bp encoding a polypeptide ob 512 amino acids, and shows sequence similarity to cadC of E. coli with 53% identity and 67% similarity. The hydrophobicity profile of the S. typhimurim CadC sequence is very similar to E. coli CadC.
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