• Journal of Life Science
• /
• v.32 no.3
• /
• pp.249-255
• /
• 2022

Metabolism is essential for survival and reproduction, and there is a metabolic pathways entry in the clusters of orthologous groups of proteins (COGs) database, updated in 2020. In this study, the metabolic pathways of 1309 prokaryotes were analyzed using COGs. There were 822 COGs associated with 63 metabolic pathways, and the mean for each taxon was between 200.50 (mollicutes) and 527.07 (cyanobacteria) COGs. The metabolic pathway composition ratio (MPCR) was defined as the number of COGs present in one genome in relation to the total number of COGs constituting each metabolic pathway, and the number of pathways with 100% MPCR ranged from 0 to 26 in each prokaryote. Among 1309 species, the 100% MPCR pathways included murein biosynthesis associated with cell wall synthesis (922 species); glycine cleavage (918); and ribosomal 30S subunit synthesis (903). The metabolic pathways with 0% MPCR were those involving photosystem I (1263 species); archaea/vacuolar-type ATP synthase (1028); and Na⁺-translocation NADH dehydrogenase (976). Depending on the prokaryote, three to 49 metabolic pathways could not be performed at all. The sequence of most highly conserved metabolic pathways was ribosome 30S subunit synthesis (96.1% of 1309 species); murein biosynthesis (86.8%); arginine biosynthesis (80.4%); serine biosynthesis (80.3%); and aminoacyl-tRNA synthesis (82.2%). Protein and cell wall synthesis have been shown to be important metabolic pathways in prokaryotes, and the results of this study of COGs related to such pathways can be utilized in, for example, the development of antibiotics and artificial cells.

• Proceedings of the Korean Information Science Society Conference
• /
• 2005.07b
• /
• pp.280-282
• /
• 2005

현재 국내외 적으로 많은 대사경로 재구축을 위한 소프트웨어들이 개발 보급되고 있다. 그러나 기존의 소프트웨어들은 유전자 서열의 주해 작업이 끝난 게놈에 대해서만 가능하다. 따라서 대사경로를 예측하고자 할 경우는 주해 작업이 선행되어야 하는 어려움이 있었다. 본 논문에서는 주해 작업이 완료되지 않은 유전자 서열로부터 유전자의 기능 예측뿐만 아니라 대사경로를 예측할 수 있는 시스템을 제안한다. 제안된 시스템은 Orthologous 데이터베이스를 활용하여 새롭게 밝혀진 유전자 서열을 대상으로 비교적 정확성이 높은 대사경로를 예측하는 기능을 제공한다. 이 방법을 통해 주해 작업이 완료되지 않은 유전자 서열을 이용하여 서열 내에 포함된 유전자의 기능을 예측할 뿐만 아니라 예측된 유전자 정보를 이용하여 대사 경로를 예측할 수 있다.

• Proceedings of the Korean Information Science Society Conference
• /
• 2004.04b
• /
• pp.295-297
• /
• 2004

유전자의 생물학적 기능을 밝히고 세포 내 상호작용을 이해하는 것은 post-genome era의 가장 중요한 작업 중 하나이다. 이러한 세포 내 상호작용은 복잡한 생화학적 네트워크를 형성하게 되며 그 중 Metabolic pathway(대사 경로)는 생물 시스템을 이해하는데 가장 중요한 부분을 차지하게 된다. 대사 경로를 분석하기 위하여 분자의 기능 및 생화학적 프로세스에 대한 정보를 데이터베이스에 저장.관리해야하고, 사용자의 다양한 질의에 대하여 관련정보를 검색하여 GUI환경에서 제공해야 한다. 이 논문은 대사 경로 정보를 객체 데이타베이스 형태로 모델링하여 구축하고, 사용자가 관심있는 정보를 SBML형태로 제공하는 대사경로 데이타베이스의 설계 및 구현에 관해 다룬다.

• Korean Journal of Poultry Science
• /
• v.37 no.3
• /
• pp.275-282
• /
• 2010

Chicken is an important livestock as a valuable biomedical model as well as food for human, and there is a strong rationale for improving our understanding on metabolism and physiology of this organism. The first draft of chicken genome assembly was released in 2004, which enables elaboration on the linkage between genetic and metabolic traits of chicken. The objectives of this study were thus to reconstruct metabolic pathway of the chicken genome and to construct a chicken specific pathway genome database (PGDB). We developed a comprehensive genome database for chicken by integrating all the known annotations for chicken genes and proteins using a pipeline written in Perl. Based on the comprehensive genome annotations, metabolic pathways of the chicken genome were reconstructed using the PathoLogic algorithm in Pathway Tools software. We identified a total of 212 metabolic pathways, 2,709 enzymes, 71 transporters, 1,698 enzymatic reactions, 8 transport reactions, and 1,360 compounds in the current chicken genome build, Gallus_gallus-2.1. Comparative metabolic analysis with the human, mouse and cattle genomes revealed that core metabolic pathways are highly conserved in the chicken genome. It was indicated the quality of assembly and annotations of the chicken genome need to be improved and more researches are required for improving our understanding on function of genes and metabolic pathways of avian species. We conclude that the chicken PGDB is useful for studies on avian and chicken metabolism and provides a platform for comparative genomic and metabolic analysis of animal biology and biomedicine.

• Proceedings of the KAIS Fall Conference
• /
• 2007.11a
• /
• pp.233-236
• /
• 2007

현재 생물정보학에서는 무수히 많은 생물들에서 엄청난 양의 EST(expressed sequence tag) 정보가 나온다. 본 논문에서는 그런 정보들을 가지고 대사경로를 유추할 수 있는 전문가 시스템을 개발하고자 한다. 현재까지의 대사경로 탐색은 발견해 놓은 데이터를 가지고 전부 수작업으로 이루어진다. 그러한 과정을 자동화 시키고자 하는 연구가 많이 진행되고 있다. 본 논문에서는 전문가 시스템을 활용하여 생물정보학의 EST(expressed sequence tag) 데이터에서 효율적으로 대사경로를 찾을 수 있도록 하는 방안을 제시한다.

• Journal of Life Science
• /
• v.28 no.3
• /
• pp.369-375
• /
• 2018

Mycoplasma genitalium has 367 conserved genes and the smallest genome among mono-culturable prokaryotes. Conservative metabolic pathways were examined among M. genitalium and 14 prokaryotes, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans and 13 intracellular eubacteria of plants or insects, with fewer conserved genes than M. genitalium. They have 11 to 71 metabolic pathways, however complete metabolic pathways ranged from 1 to 24. Totally, metabolic pathway hole is very high due to the lack of 45.8% of the enzymes required for the whole metabolic pathways and it could be suggested that the shared metabolic pathway with the host's enzyme would work or the essential substances are host dependent. The number of genes necessary for mass transfer through the cell membrane is also very low, and it may be considered that the simple diffusion or the protein of the host will function in the cell membrane of these prokaryotes. Although the tRNA charging pathway was distributed in all 15 prokaryotes, each has 5-20 tRNA charging genes. This study would give clues to the understanding of the metabolic pathways of intracellular parasitic bacteria of plant and endosymbiotic bacteria of insects, and could provide basic data for prevention of crop damage, development of insect pests and human medicines.

• Korean Journal of Microbiology
• /
• v.54 no.1
• /
• pp.46-52
• /
• 2018

Biodegradation pathway of dibenzofuran (DBF) of Novosphingobium pentaromativorans US6-1, a high-molecular-weight polycyclic aromatic hydrocarbons degrading strain, was investigated via analysis of metabolic intermediates and transcriptome. As a result, 3(2H)-benzofuranone, a basic skeleton of the metabolic intermediates produced by lateral dioxygenation process, was detected as an intermediate. RNA-Seq analysis confirmed that most of the expressed genes upon exposure to DBF were related to the lateral degradation pathway. Based on these results, the biodegradation pathway of DBF by N. pentaromativorans US6-1 was proposed.

• Proceedings of the Korean Nutrition Society Conference
• /
• 2002.05a
• /
• pp.89-89
• /
• 2002

• The Korean Journal of Zoology
• /
• v.36 no.1
• /
• pp.77-83
• /
• 1993

난모세포성숙기 (peripheral germinal vesicle stage)의 무지개송어(Oncorhynchus mykiss)를 대상으로 방사성 표지 전구체(3H-pregnenolone, 3H-l7$\alpha$-hydroxyprogesterone 그리고 3H-androstenedione)를 이용하여 유 nitro에서 관찰한 협막세포층의 스테로이드 주 대사 경로는 다음과 같으며, pregnenolone -) 17a-hydroxypregnenolone$\longrightarrow$ 17u-hydroxyprogesterone $\longrightarrow$ androstenedione $\longrightarrow$ testosterone 이는 $\Delta$5-스테로이드 경로의 존재가능성을 지적하고 있다.

• Korean Journal of Environmental Agriculture
• /
• v.15 no.2
• /
• pp.246-261
• /
• 1996

Organophosphorus pesticides, which are an important part of synthetic pesticides in current use contain sulfur atom in their molecules and can be activated or detoxified by environmental and/or biological metabolism. Among the related metabolic reactions, oxidative processes are particularly important with their final products and the study on the reactive intermediates formed in those reactions is essential to elucidate the metabolic pathways and mechanisms and to understand the toxicological properties. This review dealt with the reactive intermediates formed in various reactions from the structural and mechanistic point of view for organophosphorus pesticides and related compounds.