• Journal of Biosystems Engineering
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• 제43권1호
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• pp.45-58
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• 2018

Background: Metabolic modeling has been an essential tool in metabolic reconstruction, which has dramatically advanced in the last decades as a part of systems biology. At present, the protocol for metabolic reconstruction has been systematically established, and it provides the basis for the analysis of complex systems, which has been limited in the past. Therefore, metabolic reconstruction can be adapted to analyze agricultural systems whose metabolic data has been accumulated recently. Purpose: The aim of this review is to suggest the suitability of metabolic modeling for understanding agricultural metabolic data and to encourage the potential use of this modeling in the field of agriculture. Review: We reviewed the procedure of metabolic reconstruction using computational modeling with applicable strategies and software tools. Additionally, we presented the initial attempts of metabolic reconstruction in the field of agriculture and proposed further applications.

• Molecules and Cells
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• 제37권10호
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• pp.727-733
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• 2014

Spinosyns A and D are potent ingredient for insect control with exceptional safety to non-target organisms. It consists of a 21-carbon tetracyclic lactone with forosamine and tri-Omethylated rhamnose which are derived from S-adenosyl-methionine. Although previous studies have revealed the involvement of metK1 (S-adenosylmethionine synthetase), rmbA (glucose-1-phosphate thymidylyltransferase), and rmbB (TDP-D-glucose-4, 6-dehydratase) in the biosynthesis of spinosad, expression of these genes into rational screened Saccharopolyspora spinosa (S. spinosa MUV) has not been elucidated till date. In the present study, S. spinosa MUV was developed to utilize for metabolic engineering. The yield of spinosyns A and D in S. spinosa MUV was $244mgL^{-1}$ and $129mgL^{-1}$, which was 4.88-fold and 4.77-fold higher than that in the wild-type ($50mgL^{-1}$ and $27mgL^{-1}$), respectively. To achieve the better production; positive regulator metK1-sp, rmbA and rmbB genes from Streptomyces peucetius, were expressed and co-expressed in S. spinosa MUV under the control of strong $ermE^*$ promoter, using an integration vector pSET152 and expression vector pIBR25, respectively. Here-with, the genetically engineered strain of S. spinosa MUV, produce spinosyns A and D up to $372/217mgL^{-1}$ that is 7.44/8.03-fold greater than that of wild type. This result demonstrates the use of metabolic engineering on rationally developed high producing natural variants for the production.

• 한국산업정보학회논문지
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• 제12권4호
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• pp.138-147
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• 2007

대사 공학의 발전과 함께 생물체에 유전자 재조합기술과 관련 분자생물학 및 화학공학적 기술을 이용하여 새로운 대사회로를 도입하거나 기존의 대사회로를 제거 증폭 변경시켜 세포나 균주의 대사 특성을 조절하는(directed modification) 일련의 기술들이 가능해지고 있다. 하지만 이러한 대사회로를 조절하기 위해서는 많은 선행 연구에 대한 고찰이 필요하며, 일선 연구자들은 방대한 선행 자료를 검색하고 일일이 읽으면서 자신에게 필요한 정보를 수집하고 있다. 따라서 효율적으로 대사 모델을 구축하고, 방대한 대사관련 연구논문으로부터 대사흐름 관련 정보를 자동으로 추출하는 기술의 개발이 중요한 이슈로 부각되고 있다. 본 논문에서는 대사경로 재구축을 위한 서열과 패턴 기반의 텍스트 마이닝 기법을 제안한다. 제안된 기법은 웹 로봇을 이용하여 최신의 논문을 반자동적으로 수집하고 이를 이용하여 최신의 논문을 로컬 데이터베이스로 구축한다. 또한 생물학 개체명의 인식율을 높이기 위해 유전자 온토로지를 이용하며, NCBI에서 제공하는 Tokenizer 라이브러리를 이용하여 개체명의 파괴 없이 인식할 수 있게 하였다. 본 연구에서 제안한 텍스트 마이닝 기법에서는 패턴을 이용하여 논문으로부터 대사경로 지식을 추출하게 되므로 올바른 패턴을 확보하는 것이 중요한 문제이다. 논문에서는 패턴의 수집을 위하여 대표적인 대사 경로 전문 사이트인 일본의 KEGG 경로 데이터베이스에서 추출한 Glycosphingolip건 종에 대한 20,000 여건의 논문에서 66개의 패턴을 추출하였다. 제안된 기법의 유효성을 입증하기 위하여 Glycosphingolipid종의 GLS 대사경로 19개 개체명을 이용하여 시스템을 평가하였다. 그 결과 논문 125,907건에 대하여 정확도 96.3%, 재현을 95.1%, 처리시간 15초의 성능을 보였다. 본 논문에서 제안된 시스템은 대사 경로 재구축에 유용하게 활용될 수 있을 것으로 기대된다.

• 한국융합학회논문지
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• 제9권1호
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• pp.433-440
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• 2018

FDG PET 영상에서 MTV는 종양의 전체 대사정도를 반영하여 종양의 체적을 나타낸다. 하지만 MTV는 영상재구성의 영향을 받게 된다. 본 연구의 목적은 팬텀실험을 통하여 영상재구성에 따라 SUVmax의 역치 값을 달리하여 실제 체적과 MTV의 상관관계를 평가해보고자 하였다. NEMA IEC Body 팬텀에 $^{18}F-FDG$를 구와 배후 방사능의 비율(4:1, 8:1, 10:1, 20:1)이 되도록 주입 후 영상을 획득하였다. 획득한 영상에 4가지 방법(OSEM3D, OSEM3D+PSF, OSEM3D+TOF, OSEM3D+TOF+PSF)으로 영상을 재구성한 후 다양한 SUVmax 역치 값을 적용하여 MTV의 변화를 비교해 보았다. 전반적으로 SUVmax 역치 값이 증가 할수록 MTV가 감소하였으며, 구와 배후방사능 비율이 증가할수록 동일한 SUVmax 역치 값에서 MTV가 감소하였다. PSF와 TOF+PSF재구성영상에서 40% 역치 값, OSEM3D와 TOF 재구성 영상에서는 45% 역치 값을 적용하였을 때 팬텀의 실제체적과 MTV의 높은 상관관계를 보였다. 이번 연구결과를 통하여 영상재구성에 따라 MTV 측정에 기초적인 자료로 제공되어 질 것으로 사료된다.

• Molecules and Cells
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• 제28권4호
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• pp.397-401
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• 2009

Flavonoids are a group of polyphenolic compounds that have been recognized as important due to their physiological and pharmacological roles and their health benefits. Glycosylation of flavonoids has a wide range of effects on flavonoid solubility, stability, and bioavailability. We previously generated the E. coli BL21 (DE3) ${\Delta}pgi$ host by deleting the glucose-phosphate isomerase (Pgi) gene in E. coli BL21 (DE3). This host was further engineered for whole-cell biotransformation by integration of galU from E. coli K12, and expression of calS8 (UDP-glucose dehydrogenase) and calS9 (UDP-glucuronic acid decarboxylase) from Micromonospora echinospora spp. calichensis and arGt-4 (7-O-glycosyltransferase) from Arabidopsis thaliana to form E. coli (US89Gt-4), which is expected to produce glycosylated flavonoids. To test the designed system, the engineered host was fed with naringenin as a substrate, and naringenin 7-O-xyloside, a glycosylated naringenin product, was detected. Product was verified by HPLC-LC/MS and ESI-MS/MS analyses. The reconstructed host can be applied for the production of various classes of glycosylated flavonoids.

• 한국유전체학회:학술대회논문집
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• 한국유전체학회 2006년도 The 15th Korean Genome Organization Conference KOGO 2006 Annual Meeting
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• pp.35-35
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• 2006

• KSBB Journal
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• 제24권3호
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• pp.287-290
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• 2009

최근 미생물을 이용하여 기존에 화학산업을 통하여 생산되어지던 여러 화학물질 혹은 대사산물을 생산하려는 연구가 활발히 이루어지고 있다. 이러한 연구를 통하여 미생물의 대사특성을 개량하기 위하여는, 미생물의 대사 특성을 분석하는 연구가 일차적으로 수행되어져야 한다. 본 연구에서는 대사network간의 기능적 연관성을 분석하기 위하여 transcriptome 연구에 주로 활용되던 ARACNE 기법이 활용되었다. 특정 대사 subpathway들이 미생물 균주들 사이에 존재하는 패턴이 유사하다면 그 대사 subpathway들이 서로 기능적 상관관계를 가지고 있을 가능성이 높다는 가정 하에, ARACNE를 활용하여 미생물들의 subrathway들의 존재 패턴을 분석함으로서 각 subpathway 사이의 기능적 상관관계를 분석하여 보았다. 본 연구에 활용된 새로운 대사network 분석기법을 활용한다면 더욱 효율적인 대사network 분석연구가 수행될 수 있을 것이라 기대된다.

• Journal of Microbiology and Biotechnology
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• 제21권11호
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• pp.1143-1146
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• 2011

Metabolic engineering of plant-specific phenylpropanoid biosynthesis has attracted an increasing amount of attention recently, owing to the vast potential of flavonoids as nutraceuticals and pharmaceuticals. Recently, we have developed a recombinant Streptomyces venezuelae as a heterologous host for the production of flavonoids. In this study, we successfully improved flavonoid production by expressing two sets of genes predicted to be involved in malonate assimilation. The introduction of matB and matC encoding for malonyl-CoA synthetase and the putative dicarboxylate carrier protein, respectively, from Streptomyces coelicolor into the recombinant S. venezuelae strains expressing flavanone and flavone biosynthetic genes resulted in enhanced production of both flavonoids.

• Journal of Veterinary Science
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• 제19권6호
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• pp.798-807
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• 2018

Several studies have reported the effect of absorption of procyanidins and their contribution to the small intestine. However, differences between dietary interventions of procyanidins and interventions via antibiotic feeding in pigs are rarely reported. Following 16S rRNA gene Illumina MiSeq sequencing, we observed that both procyanidin administration for 2 months (procyanidin-1 group) and continuous antibiotic feeding for 1 month followed by procyanidin for 1 month (procyanidin-2 group) increased the number of operational taxonomic units, as well as the Chao 1 and ACE indices, compared to those in pigs undergoing antibiotic administration for 2 months (antibiotic group). The genera Fibrobacter and Spirochaete were more abundant in the antibiotic group than in the procyanidin-1 and procyanidin-2 groups. Principal component analysis revealed clear separations among the three groups. Additionally, using the online Molecular Ecological Network Analyses pipeline, three co-occurrence networks were constructed; Lactobacillus was in a co-occurrence relationship with Trichococcus and Desulfovibrio and a co-exclusion relationship with Bacillus and Spharerochaeta. Furthermore, metabolic function analysis by phylogenetic investigation of communities by reconstruction of unobserved states demonstrated modulation of pathways involved in the metabolism of carbohydrates, amino acids, energy, and nucleotides. These data suggest that procyanidin influences the gut microbiota and the intestinal metabolic function to produce beneficial effects on metabolic homeostasis.

• 한국축산식품학회지
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• 제35권5호
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• pp.692-702
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• 2015

Lactobacillus mucosae is a natural resident of the gastrointestinal tract of humans and animals and a potential probiotic bacterium. To understand the global protein expression profile and metabolic features of L. mucosae LM1 in the early stationary phase, the QExactive^TM Hybrid Quadrupole-Orbitrap Mass Spectrometer was used. Characterization of the intracellular proteome identified 842 proteins, accounting for approximately 35% of the 2,404 protein-coding sequences in the complete genome of L. mucosae LM1. Proteome quantification using QExactive^TM Orbitrap MS detected 19 highly abundant proteins (> 1.0% of the intracellular proteome), including CysK (cysteine synthase, 5.41%) and EF-Tu (elongation factor Tu, 4.91%), which are involved in cell survival against environmental stresses. Metabolic pathway annotation of LM1 proteome using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database showed that half of the proteins expressed are important for basic metabolic and biosynthetic processes, and the other half might be structurally important or involved in basic cellular processes. In addition, glycogen biosynthesis was activated in the early stationary phase, which is important for energy storage and maintenance. The proteogenomic data presented in this study provide a suitable reference to understand the protein expression pattern of lactobacilli in standard conditions