Publications
Detailed Information
Genome-Scale Reconstruction of OxyR, OxyR-2 Transcriptional Regulatory Networks in Methylomonas sp. DH-1 : 메탄자화균 DH-1의 OxyR, OxyR-2 전사조절 네트워크 규명
DC Field | Value | Language |
---|---|---|
dc.contributor.advisor | 서상우 | - |
dc.contributor.author | 김범희 | - |
dc.date.accessioned | 2019-05-07T03:22:38Z | - |
dc.date.available | 2019-05-07T03:22:38Z | - |
dc.date.issued | 2019-02 | - |
dc.identifier.other | 000000153949 | - |
dc.identifier.uri | https://hdl.handle.net/10371/150844 | - |
dc.description | 학위논문 (석사)-- 서울대학교 대학원 : 공과대학 협동과정 바이오엔지니어링전공, 2019. 2. 서상우. | - |
dc.description.abstract | Industrial uses and needs for methane is increasing nowadays since it has industrial utility and cost-efficiency. Methanotrophs can utilizes methane as a sole carbon source for the bioconversion to methanol or various value-added chemicals. Methylomonas sp. DH-1 is a promising industrial strain since it has relatively high specific growth rate and methanol resistance among methanotrophs. However, there is a lack of biological and technological bases for the engineering of methanotrophs. In this study, multi-omics analysis for OxyR and OxyR-2 was conducted in Methylomonas sp. DH-1 for oxidation response, which is essential to cells. The OxyR binding motif was discovered from ChIP-seq. From RNA-seq, 439 and 190 genes under normal condition, 52 and 176 genes under the oxidative stress were discovered as candidate genes for OxyR, OxyR-2 regulons, respectively. Moreover, the regulatory causation between genomic TF binding and the regulation of energy metabolism, inorganic ion transport, amino acid biosynthesis, and cell wall synthesis were discovered. | - |
dc.description.abstract | 최근 셰일가스의 생산기술의 발달과 함께 메탄은 그 생산량과 소비량이 늘어나는 추세에 있으며 다양한 활용성과 경제성으로 차세대 에너지원으로써 각광받고 있다. 메탄자화균은 메탄을 주탄소원으로하여 메탄올로의 효율적인 전환 및 다양한 고부가가치 화합물 생산에 활용될 수 있다는 장점이 있다. 특히, Methylomonas sp. DH-1은 메탄자화균 중에서 비교적 높은 비성장속도, 메탄올 저항성을 가지므로 대사공학을 통해 산업적으로 활용되기 위한 가능성이 높은 균주이다. 그러나 기존 산업미생물을 대체하여 메탄자화균을 활용하기 위한 기술과 생물학적 기반은 매우 부족한 상태이다. 본 연구에서는 미생물 내에서의 핵심 전사조절기작 중의 하나인 산화 스트레스와 관련하여, Methylomonas sp. DH-1 내의 전사인자 OxyR, OxyR-2 에 대한 융합오믹스 분석을 수행하였다. 전사체 분석 및 상호작용체 분석을 통해 에너지 대사, 무기질 이온 수송, 아미노산 생합성, 세포벽 합성 경로가 OxyR과 OxyR-2과 관련된 조절적 인과관계를 갖는 것으로 밝혀졌으며, 두 전사인자의 레귤론에 속하는 유전자를 각각 4개, 1개 발굴해낼 수 있었다. 추가적으로 OxyR의 유전체 결합 모티프를 찾아냈으며, OxyR, OxyR-2 레귤론 후보군으로 추정되는 유전자를 일반 배양 조건에서 439개, 190개, 산화 스트레스 조건에서 52개, 176개를 발굴하였다. | - |
dc.description.tableofcontents | Chapter 1. Introduction 1
1.1 The Potential of Methanotrophs as an Industrial Strains for the Bioprocess 1 1.2 Methylomonas sp. DH-1 as a Promising Industrial Strain 2 1.3 Oxidation Responses and Transcriptional Regulator OxyR in Bacteria 4 1.4 The Scope of This Research 5 Chapter 2. Materials and Methods 6 2.1 Bacterial Strains, Media, and Culture Conditions 6 2.2 Design and Construction of Linker-Myc-kanR Cassette 6 2.3 Preparation of Recombination DNA Fragments for the Construction of Methylomonas sp. DH-1 ΔoxyR and ΔoxyR-2 Mutants 9 2.4 Preparation of Recombination DNA Fragments for the Construction of Methylomonas sp. DH-1 OxyR-Myc and OxyR-2-Myc Mutants 10 2.5 Electroporation-Based Transformation in Methylomonas sp. DH-1 11 2.6 RNA-Seq and Differential Expression Analysis 11 2.7 ChIP-Seq and Genomic Binding Motif Analysis 13 Chapter 3. Results and Discussion 16 3.1 Identification of oxyR, oxyR-2 Genes in Methylomonas sp. DH-1 Genome 16 3.2 Construction of Mutant Strains for Omics Analyses 16 3.3 Differential Expression Analyses under the Normal Condition and the Exposure to Redox-Cycling Agents 18 3.4 Epitope Tagging Strategy on Methylomonas sp. DH-1 22 3.5 Genomic Binding Motif Search 24 3.6 OxyR, OxyR-2 Regulons in Methylomonas sp. DH-1 26 Chapter 4. Conclusion 28 References 30 Supplements 36 Abstract in Korean 67 | - |
dc.language.iso | eng | - |
dc.publisher | 서울대학교 대학원 | - |
dc.subject.ddc | 660.6 | - |
dc.title | Genome-Scale Reconstruction of OxyR, OxyR-2 Transcriptional Regulatory Networks in Methylomonas sp. DH-1 | - |
dc.title.alternative | 메탄자화균 DH-1의 OxyR, OxyR-2 전사조절 네트워크 규명 | - |
dc.type | Thesis | - |
dc.type | Dissertation | - |
dc.contributor.AlternativeAuthor | Beomhee Kim | - |
dc.description.degree | Master | - |
dc.contributor.affiliation | 공과대학 협동과정 바이오엔지니어링전공 | - |
dc.date.awarded | 2019-02 | - |
dc.identifier.uci | I804:11032-000000153949 | - |
dc.identifier.holdings | 000000000026▲000000000039▲000000153949▲ | - |
- Appears in Collections:
- Files in This Item:
Item View & Download Count
Items in S-Space are protected by copyright, with all rights reserved, unless otherwise indicated.