Journal of Microbiology

Jae-Seong So

8 Articles

Role of the extracytoplasmic function sigma factor CarQ in oxidative response of Bradyrhizobium japonicum: Anchana Thaweethawakorn , Dylan Parks , Jae-Seong So , Woo-Suk Chang; J. Microbiol. 2015;53(8):526-534. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5308-9

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As a nitrogen-fixing bacterium, Bradyrhizobium japonicum can establish a symbiotic relationship with the soybean plant (Glycine max). To be a successful symbiont, B. japonicum must deal with plant defense responses, such as an oxidative burst. Our previous functional genomics study showed that carQ (bll1028) encoding extracytoplasmic function (ECF) sigma factor was highly expressed (107.8-fold induction) under oxidative stress. Little is known about the underlying mechanisms of how CarQ responds to oxidative stress. In this study, a carQ knock-out mutant was constructed using site-specific mutagenesis to identify the role of carQ in the oxidative response of B. japonicum. The carQ mutant showed a longer generation time than the wild type and exhibited significantly decreased survival at 10 mM H2O2 for 10 min of exposure. Surprisingly, there was no significant difference in expression of oxidative stress-responsive genes such as katG and sod between the wild type and carQ mutant. The mutant also showed a significant increase in susceptibility to H2O2 compared to the wild type in the zone inhibition assay. Nodulation phenotypes of the carQ mutant were distinguishable compared to those of the wild type, including lower numbers of nodules, decreased nodule dry weight, decreased plant dry weight, and a lower nitrogen fixation capability. Moreover, desiccation of mutant cells also resulted in significantly lower percent of survival in both early (after 4 h) and late (after 24 h) desiccation periods. Taken together, this information will provide an insight into the role of the ECF sigma factor in B. japonicum to deal with a plant-derived oxidative burst.

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Implication of the σ E Regulon Members OmpO and σ N in the Δ ompA 299–356 -Mediated Decrease of Oxidative Stress Tolerance in St
Ren-Hsuan Ku, Li-Hua Li, Yi-Fu Liu, En-Wei Hu, Yi-Tsung Lin, Hsu-Feng Lu, Tsuey-Ching Yang, Silvia T. Cardona
Microbiology Spectrum.2023;[Epub] CrossRef
Identification and Validation of Reference Genes for Expression Analysis in Nitrogen-Fixing Bacteria under Environmental Stress
Dylan Parks, Christian Peterson, Woo-Suk Chang
Life.2022; 12(9): 1379. CrossRef
MostSinorhizobium melilotiExtracytoplasmic Function Sigma Factors Control Accessory Functions
Claus Lang, Melanie J. Barnett, Robert F. Fisher, Lucinda S. Smith, Michelle E. Diodati, Sharon R. Long, Craig D. Ellermeier, Claude Bruand, Sarah Ades, Hans-Martin Fischer
mSphere.2018;[Epub] CrossRef

Reductive Dechlorination of Polychlorinated Biphenyls as Affected by Natural Halogenated Aromatic Compounds: Jongseol Kim , Ahmi Lee , Yong-Suk Moon , Jae-Seong So , Sung-Cheol Koh; J. Microbiol. 2006;44(1):23-28.; DOI: https://doi.org/2341 [pii]

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Abstract PDF: We investigated the effects of halogenated aromatic compounds (HACs) including naturally occurring ones (L-thyroxine, 3-chloro-L-tyrosine, 5-chloroindole, 2-chlorophenol, 4-chlorophenol and chlorobenzene) on polychlorinated biphenyl (PCB) dechlorination in sediment cultures. A PCB-dechlorinating enrichment culture of sediment microorganisms from the St. Lawrence River was used as an initial inoculum. When the culture was inoculated into Aroclor 1248 sediments amended with each of the six HACs, the extent of dechlorination was not enhanced by amendment with HACs. The dechlorination patterns in the HAC-amended sediments were nearly identical to that of the HAC-free sediments except the 3-chloro-L-tyrosine-amended ones where no dechlorination activity was observed. When these sediment cultures were transferred into fresh sediments with the same HACs, the dechlorination specificities remained the same as those of the initial inoculations. Thus, in the present study, the substrate range of the highly selected enrichment culture could not be broadened by the HACs. It appears that HACs affect PCB dechlorination mainly through population selection rather than enzyme induction of single population.

Green Fluorescent Protein as a Marker for Monitoring a Pentachlorophenol Degrader Sphingomonas chlorophenolica ATCC39723: Eun-Taex Oh , Jae-Seong So , Byung-Hyuk Kim , Jong-Sul Kim , Sung-Cheol Koh; J. Microbiol. 2004;42(3):243-247.; DOI: https://doi.org/2081 [pii]

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Abstract PDF: Sphingomonas chlorophenolica ATCC39723 was successfully labeled with the gfp (green fluorescent protein) gene inserted into the pcpB gene by homologous recombination. As the gfp recombinant was easily distinguished from other indigenous organisms, the population of gfp recombinant was monitored after being released into the soil microcosms. Their population density dropped from 108 to 106 (cfu/ml) in the non-sterilized soil microcosms during the first 6 days. Moreover, the gfp recombinant was not detected even at lower dilution rates after a certain time period. The recombinant, however, survived for at least 28 days in the sterilized soil microcosms. Although the gfp recombinant did not degrade pentachlorophenol (PCP), this experiment showed the possibility of using gfp as a monitoring reporter system for S. chlorophenolica ATCC39723 and potentially other species of Sphingomonas.

Molecular Cloning and Identification of a Novel Oxygenase Gene Specifically Induced during the Growth of Rhodococcus sp. Strain T104 on Limonene: Ki Young Choi , Dockyu Kim , Sung-Cheol Koh , Jae-Seong So , Jong-Sul Kim , Eungbin Kim; J. Microbiol. 2004;42(2):160-162.; DOI: https://doi.org/2027 [pii]

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Abstract PDF: Rhodococcus sp. strain T104 is able to utilize both limonene and biphenyl as growth substrates.Furthermore, T104 possesses separate pathways for the degradation of limonene and biphenyl. Previously, we found that a gene(s) involved in limonene degradation was also related to indigo-producing ability. To further corroborate this observation, we have cloned and sequenced a 8,842-bp genomic DNA region with four open reading frames, including one for indole oxygenase, which converts indole to indigo (a blue pigment). The reverse transcription PCR data demonstrated that the identified indole oxygenase gene is specifically induced by limonene, thereby implicating this gene in the degradation of limonene by T104.

Plant Terpene-Induced Expression of Multiple Aromatic Ring Hydroxylation Oxygenase Genes in Rhodococcus sp. Strain T104: Byung-Hyuk Kim , Eun-Taex Oh , Jae-Seong So , Yeonghee Ahn , Sung-Cheol Koh; J. Microbiol. 2003;41(4):349-352.

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Abstract PDF: Recent studies have shown that some of the PCB (polychlorinated biphenyl)-degraders are able to effectively degrade PCB in the presence of monoterpenes, which act as inducers for the degradation pathway. Rhodococcus sp. T104, an effective PCB degrader, has been shown to induce the degradation pathway by utilizing limonenes, cymenes, carvones, and pinenes as sole carbon sources which can be found in the natural environment. Moreover, the strain T104 proved to possess three separate oxidation pathways of limonene, biphenyl, and phenol. Of these three, the limonene can also induce the biphenyl degradation pathway. In this work, we report the presence of three distinct genes for aromatic oxygenase, which are putatively involved in the degradation of aromatic substrates including biphenyl, limonene, and phenol, through PCR amplification and denaturing gradient gel electrophoresis (DGGE). The genes were differentially expressed and well induced by limonene, cymene, and plant extract A compared to biphenyl and/or glucose. This indicates that substrate specificity must be taken into account when biodegradation of the target compounds are facilitated by the plant natural substrates.

Isolation and Identification of a Pentachloronitrobenzene (PCNB) Degrading Bacterium Alcaligenes xylosoxidans PCNB-2 from Agricultural Soil: Sung-Kyu Shin , Jang-Eok Kim , Gi-Seok Kwon , Jin-Wook Kwon , Eun-Taex Oh , Jae-Seong So , Sung-Cheol Koh; J. Microbiol. 2003;41(2):165-168.

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Abstract PDF: We report a new PCNB-degrading strain (PCNB-2) that is able to utilize and grow on PCNB (100 ppm) as a sole carbon source. This strain was identified as Alcaligenes xylosoxidans based upon 16S rDNA sequence analysis, API 20 NE tests and cell membrane lipid analysis. The new PCNB degrader Alcali-genes xylosoxidans PCNB-2 could find use in bioremediation of PCNB, which is environmentally persistent.

Monitoring Expression of bphC Gene from Ralstonia eutropha H850 Induced by Plant Terpenes in Soil: Kyung-Ja Jung , Byung-Hyuk Kim , Eungbin Kim , Jae-Seong So , Sung-Cheol Koh; J. Microbiol. 2002;40(4):340-343.

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Abstract PDF: A PCB degrader, Ralstonia eutropha H850 was shown to induce bphC gene encoding 2,3-dihydroxy-biphenyl-1,2-dioxygenase in a carvone-amended pure culture in our previous study (Park et al., 1999). The present study was carried out to examine how plant terpenes, as natural substrates, would cause an expression of a PCB degradative gene in soil that was amended with terpenes. The population of Ralstonia eutropha H850 was maintained at least around 10 8 (CFU/g fresh soil) in the soil amended with carvone or limonene in the presence of succinate as a growth substrate at 50 th day. The gene expression was monitored by RT-PCR using total RNA directly extracted from each soil and bphC gene primers. The bphC gene expression of the seeded strain H850 was observed in the soil amended with biphenyl (4 days) but not with succinate, carvone and limonene. These results indicate that terpenes widely distributed in nature could be a potential inducing substrate for effective PCB biodegration in the soil but their bioavailability and specific induction behavior should be taken into account before PCB bioremediation implementation.

Three Separate Pathways for the Initial Oxidation of Limonene, Biphenyl, and Phenol by Rhodococcus sp. Strain T104: Dockyu Kim , Min Jung Park , Sung-Cheol Koh , Jae-Seong So , Eungbin Kim; J. Microbiol. 2002;40(1):86-89.

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Abstract PDF: Rhodococcus sp. strain T104, which is able to grow on either biphenyl or limonene, was found to utilize phenol as sole carbon and energy sources. Furthermore, T104 was positively identified to possess three separate pathways for the degradation of limonene, phenol, and biphenyl. The fact that biphenyl and limonene induced almost the same amount of catechol 1,2-dioxygenase activity indicates that limonene can induce both upper and lower pathways for biphenyl degradation by T104.

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