• Journal of Microbiology and Biotechnology
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• 제14권1호
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• pp.74-80
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• 2004

Aspergillus fumigatus is one of the most common fungi in the human environment, both in-doors and out-doors. It is the main causative agent of invasive aspergillosis, a life-threatening mycosis among immunocompromised patients. The genome has been sequenced by an international consortium, including the Wellcome Trust Sanger Institute (U.K.) and The Institute for Genomic Research (TIGR, U.S.A.), and a ten times whole genome shotgun sequence assembly has been made publicly available. In this study, we identified tricarboxylic acid (TCA) cycle enzymes of A. fumigatus by comparative analysis with four other fungal species. The open reading frames showed high amino acid sequence similarity with the other fungal citric acid enzymes and well-conserved functional domains. All genes present in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, and Neurospora crassa were also found in A. fumigatus. In addition, we identified four A. fumigatus genes coding for enzymes in the glyoxylate shunt, which may be required for fungal virulence. The architecture of multi-gene encoded enzymes, such as isocitrate dehydrogenase, 2-ketoglutarate, succinyl-CoA synthetase, and succinate dehydrogenase was well conserved in A. fumigatus. Furthermore, our results show that genes of A. fumigatus can be detected reliably using GlimmerM.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2006년도 한국컴퓨터종합학술대회 논문집 Vol.33 No.1 (A)
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• pp.4-6
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• 2006

Tree-dependent component analysis (TCA) is a generalization of independent component analysis (ICA), the goal of which is to model the multivariate data by a linear transformation of latent variables, while latent variables fit by a tree-structured graphical model. In contrast to ICA, TCA allows dependent structure of latent variables and also consider non-spanning trees (forests). In this paper, we present a TCA-based method of clustering gene expression data. Empirical study with yeast cell cycle-related data, yeast metaboiic shift data, and yeast sporulation data, shows that TCA is more suitable for gene clustering, compared to principal component analysis (PCA) as well as ICA.

• Journal of Microbiology and Biotechnology
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• 제16권7호
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• pp.1158-1162
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• 2006

The glyoxylate cycle can conserve carbons and adequately supply tricarboxylic acid (TCA) cycle intermediates for biosynthesis when microorganisms grow on $C_{2}$ carbon sources. It has been reported that isocitrate lyase (ICL1), a key enzyme of the glyoxylate cycle, is highly induced when Magnaporthe grisea, the causal agent of rice blast, infects its host. Therefore, the glyoxylate cycle is considered as a new target for antifungal agents. A 1.6-kb DNA fragment encoding the ICL1 from M. grisea KJ201 was amplified by PCR, cloned into a vector providing His-tag at the N-terminus, expressed in Escherichia coli, and purified using Ni-NTA affinity chromatography. The molecular mass of the purified ICL1 was approximately 60 kDa, as determined by SDS-PAGE. The ICL1 inhibitory effects of TCA cycle intermediates and their analogs were investigated. Among them, 3-nitropropionate was found to be the strongest inhibitor with an $IC_{50}$ value of $11.0{\mu}g/ml$. 3-Nitropropionate inhibited the appressorium development in M. grisea at the ${\mu}M$ level, whereas conidia germination remained unaffected. This compound also inhibited the mycelial growth of the fungus on minimal medium containing acetate as a $C_{2}$ carbon source. These results suggest that ICL1 plays a crucial role in appressorium formation of M. grisea and is a new target for the control of phytopathogenic fungal infection.

• Korean Chemical Engineering Research
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• 제55권3호
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• pp.363-368
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• 2017

메탄올자화균이란 일탄소 화합물인 메탄올을 주탄소원 및 에너지원으로 이용할 수 있는 미생물을 말한다. Methylobacterium extorquens AM1은 serine cycle을 탄소대사경로로 이용하는 메탄올자화균 중에서도 가장 많이 연구가 진행된 균주이다. M. extorquens AM1의 poly 3-hydroxybutyrate (PHB) cycle은 EMCP (ethylmalonyl-CoA pathway), glyoxylate regeneration cycle, TCA cycle과 연결되어 있으며 EMCP 유래 유기산 또는 TCA 유기산을 생산하기 위해서는 PHB cycle로 흐르는 carbon flux의 차단이 필요하다. 이를 위해서 PHB 합성과 acetyl-CoA flux의 조절유전자로 알려져 있는 PhaR 유전자를 markerless gene deletion 방법을 이용해서 M. extorquens AM1에서 knockout했다. 결과적으로, knockout 균주인 ${\Delta}phaR$에서 야생종 대비 확연히 PHB granule이 줄어든 것이 확인되었다. Lag phase가 약 12 h 늦어졌지만, ${\Delta}phaR$은 야생종과 비슷한 세포성장과 메탄올소비 경향을 보임을 확인하였다.

• 전자공학회논문지
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• 제50권12호
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• pp.98-106
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• 2013

에너지 수확 모바일 센서 망에서 센서 노드간의 듀티-사이클 동기화는 매우 중요한 의미를 갖는다. 제한된 에너지를 효율적으로 사용하여 협력해야 하기 때문에 각 노드의 듀티-사이클이 서로 유사하게 동작되어야 한다. 이때 망을 구성하는 노드분포는 노드간의 연결뿐만 아니라 동기화에 의한 노드의 활동 시간, 그리고 망의 수명에 영향을 준다. 본 논문에서는 자기-동기화 듀티-사이클 기법을 적용한 에너지 수확 모바일 센서 망에서 망의 토폴로지를 변화시킨다. 단순 랜덤 토폴로지 망보다는 망이 담당하는 영역과 노드 밀집도에 따라서 노드의 분포를 균일하게 유지하는 알고리즘을 제시한다. 제시된 토폴로지 변환 알고리즘을 위하여 유체 흐름과 군집 분산 모델을 적용하고 에이전트 기반 모델링을 이용하여 성능분석을 시행한다. 또한 제안된 알고리즘을 자기-동기화 듀티-사이클 기반 모바일 센서 망에 적용하여 노드 간 동기화 특성이 강화되고 에너지 소비 편차의 감소를 확인한다.

• Journal of Microbiology and Biotechnology
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• 제19권1호
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• pp.23-36
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• 2009

In the present work, the metabolic network of primary metabolism of the slow-growing myxobacterium Sorangium cellulosum was reconstructed from the annotated genome sequence of the type strain So ce56. During growth on glucose as the carbon source and asparagine as the nitrogen source, So ce56 showed a very low growth rate of $0.23\;d^{-1}$, equivalent to a doubling time of 3 days. Based on a complete stoichiometric and isotopomer model of the central metabolism, $^{13}C$ metabolic flux analysis was carried out for growth with glucose as carbon and asparagine as nitrogen sources. Normalized to the uptake flux for glucose (100%), cells recruited glycolysis (51%) and the pentose phosphate pathway (48%) as major catabolic pathways. The Entner-Doudoroff pathway and glyoxylate shunt were not active. A high flux through the TCA cycle (118%) enabled a strong formation of ATP, but cells revealed a rather low yield for biomass. Inspection of fluxes linked to energy metabolism revealed that S. cellulosum utilized only 10% of the ATP formed for growth, whereas 90% is required for maintenance. This explains the apparent discrepancy between the relatively low biomass yield and the high flux through the energy-delivering TCA cycle. The total flux of NADPH supply (216%) was higher than the demand for anabolism (156%), indicating additional reactions for balancing of NADPH. The cells further exhibited a highly active metabolic cycle, interconverting $C_3$ and $C_4$ metabolites of glycolysis and the TCA cycle. The present work provides the first insight into fluxes of the primary metabolism of myxobacteria, especially for future investigation on the supply of cofactors, building blocks, and energy in myxobacteria, producing natural compounds of biotechnological interest.

• Journal of Microbiology and Biotechnology
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• 제23권7호
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• pp.923-931
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• 2013

Rapamycin, known as an inhibitor of Target of Rapamycin (TOR), is an immunosuppressant drug used to prevent rejection in organ transplantation. Despite the close association of the TOR signaling cascade with various scopes of metabolism, it has not yet been thoroughly investigated at the metabolome level. In our current study, we applied mass spectrometric analysis for profiling primary metabolism in order to capture the responsive dynamics of the Chlamydomonas metabolome to the inhibition of TOR by rapamycin. Accordingly, we identified the impact of the rapamycin treatment at the level of metabolomic phenotypes that were clearly distinguished by multivariate statistical analysis. Pathway analysis pinpointed that inactivation of the TCA cycle was accompanied by the inhibition of cellular growth. Relative to the constant suppression of the TCA cycle, most amino acids were significantly increased in a time-dependent manner by longer exposure to rapamycin treatment, after an initial down-regulation at the early stage of exposure. Finally, we explored the isolation of the responsive metabolic factors into the rapamycin treatment and the culture duration, respectively.

• Journal of Microbiology and Biotechnology
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• 제6권2호
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• pp.120-127
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• 1996

The characteristics of cell growth and poly-$\beta$-hydroxybutyrate biosynthesis of Alcaligenes latus ATCC 29713 were investigated. The PHB accumulation pattern of A. latus followed a growth-associated type where the cell growth and PHB accumulation were carried out simultaneously. Various intermediate compounds such as metabolites involved in the TCA cycle, amino acids, and saturated and unsaturated fatty acids were added to examine their effect on cell growth and PHB accumulation. Citrate, tyrosine, and palmitic acid showed the most significant increase both on cell growth and PHB accumulation. Maximum PHB concentrations were noticeably increased about 1.4 to 1.6 times higher than that of control, corresponding to 5.54, 6.45, and 6.45 g/l for citrate, tyrosine, and palmitic acid, respectively. The stimulatory effects of the supplemented metabolites were analyzed in terms of the increment of enzyme activities related to sugar catabolism and PHB biosynthesis.

• Journal of Applied Biological Chemistry
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• 제42권1호
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• pp.1-6
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• 1999

Poly-${\beta}$-hydroxybutyrate (PHB) and enzymes related PHB metabolism have been measured in nitrogen-fixing symbiosis of chickpea and cowpea plants. Bacteroids from chickpea and cowpea contained PHB to 0.8% and 43% of their dry weight, respectively, whereas the free-living cells CC 1192 and I 16 produced $285{\pm}55mg$ and $157{\pm}18mg$ of PHB g (dry weight)$^{-1}$. To further understand why chickpea bacteroids contained little PHB, the enzyme activities of PHB metabolism (3-ketothiolase, acetoacetyl-CoA reductase, PHB depolymerase, and 3-hydroxybutyrate dehydrogenase), the TCA cycle (malate dehydrogenase, citrate synthase, and isocitrate dehydrogenase), and related reactions (malic enzyme, pyruvate dehydrogenase, and glutamate:2-oxoglutarate transaminase) were compared in extracts from chickpea and cowpea bacteroids and the respective free-living bacteria. Significant differences were observed between chickpea and cowpea bacteroids and between the bacteroid and free-living forms of CC 1192, with respect to the capacity for some of these reactions. It is indicated that a greater potential for oxidizing malate to oxaloacetate in chickpea bacteroids could be a factor that favors the utilization of acetyl-CoA in TCA cycle rather than for PHB synthesis.

• KSBB Journal
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• 제18권2호
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• pp.94-99
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• 2003

Gluconacetobacter hansenii PJK의 경우 배지 조성 중 탄소원보다는 질소원 및 acetic acid가 BC 생산에 더 많은 영향을 미쳤다. 또한 BC 생산능은 pH 4.1-6.0 범위에서 배지의 초기 pH 영향을 거의 받지 않았으며 BC에 둘러싸인 균주보다 배양 상등액에 존재하는 균주의 BC 생산능이 더 우수하였다. G. hansenii PJK의 BC 생산은 fructose metabolism이 아닌 glucose metabolism으로 이루어지며 배지 성분 중 fructose와 lactate는 Cel$^{-}$ mutant의 발생 및 성장을 촉진시켰으며 TCA cycle에 위치하는 succinate의 첨가는 BC 생산에 거의 영향을 미치지 않았다.