Omics Approach to Understand the Formation of Colony Boundar
发布时间：2025-01-20 13:21
各种各样的细菌生活在同一个微生物群落中,它们需要在有限的空间和资源之中进行激烈的竞争或合作。相互合作的细胞可以产生大量有利于其自身生存的行为,包括营养的获得、群体运动、毒力、防御、离子吸收、生物膜形成以及子实体形成。为了确保这些合作行为发生在同种细胞之间,细菌需要被相邻的细胞所识别。微生物社会学直接受到邻近细胞的协同或对抗行为的影响,这些行为基于微生物自我识别和非自我排除以形成相关群落的能力。细菌中细胞间的亲缘识别通常表现为菌落融合不兼容,直到目前,有一些关于菌落融合不兼容的研究认为,同类菌株的两个菌落相遇后可以融合,而两个非同类菌株的菌落相遇后会形成一条肉眼可见的界线。一些细菌物种的近亲,例如奇异变形杆菌、枯草芽孢杆菌和黄色粘球菌,能够在彼此无法识别的不同菌株的菌落之间形成可见的界线,这就是菌落融合不兼容现象。黄色粘球菌DK1622是一种革兰氏阴性土壤细菌,属于变形杆菌（Proteobacteria）的δ分枝,该模式菌株的基因组己完全测序。黄色粘球菌的独特特征之一是它具有多细胞行为且是众所周知的社会性细菌,例如在营养丰富的固体表面上,它具有细胞的群体运动能力,而在营养成分稀少的情况下,...
【文章页数】：190 页
【学位级别】：博士
【文章目录】：
摘要
Abstract
Chapter 01 INTRODUCTON
1. Overview
1.1 PROTEOMIC
1.1.1 An overview of proteomic approaches
1.1.2 Post-Translation Modifications
1.1.3 Mass Spectrometry-based Proteomics
1.1.4 Database Searching and Protein Identification
1.1.5 Application of proteomics (overview)
1.2 METABOLOMICS
1.2.1 Overview of metabolomics
1.2.2 Advantages of metabolomics
1.2.3 Metabolomics techniques
1.2.4 Applications of metabolomics
1.3 MYXOBACTERIA
1.3.1 Overview of myxobacteria
1.3.2 Diversity and ecology
1.3.3 Myxobacterial genome
1.3.4 Social interactions
1.3.5 Predation
1.3.6 Production of natural products
1.4 COLONY-MERGE INCOMPATIBILITY
1.4.1 Overview of boundary formation
1.4.2 Balance in colony boundaries
1.4.3 Mechanism of colony merging incompatibility
1.5 AIM AND OBJECTIVES
Chapter 02 MATERIAL AND METHODS
2.1 Materials and chemicals
2.1.1 Reagents preparation
2.1.2 Medium and reagents
2.1.3 Apparatus and instruments
2.1.4 Strains and plasmids
2.1.5 List of primers
2.2 Experimental methods
2.2.1 Fluorescence microscopy observation of colony boundaries
2.2.2 Scanning Electron Microscopy (SEM)
2.2.3 Sample preparation for LC-MS/MS
2.2.3.1 Purification of digested proteins and peptides by Zip-Tip
2.2.4 Nano-LC-LTQ-Orbitrap parameters and data processing
2.2.5 Sample preparation and extraction of compounds from boundary
2.2.6 High-resolution HPLC-MS/MS system parameters
2.2.7 T6SS-knockout sample preparation
2.3 Data analysis
Chapter 03 RESULTS
3.1 Role of MXAN-0049 gene in colony boundary formation
3.2 Colony boundaries between incompatible M. xanthus strains under microscope
3.3 Proteomic analysis of colony boundaries
3.3.1 Significantly expressed protein within boundary
3.3.2 Gene ontology of boundary
3.3.3 Significance proteins and their co-relation with boundary formation
3.3.4 Proteomics analysis and KEGG pathways
3.3.5 Role of Protein Export pathway in boundary
3.3.6 Interaction of Cold shock proteinswith RNA degmdation pathway
3.3.7 Co-relationships of boundary formation with T6SS system
3.3.8 Phenylalanine, tyrosine and tryptophan biosynthesis
3.4 Identification of chemical compounds by HPLC-MS/MS
3.4.1 antiSMASH prediction of gene cluster and boundary
3.4.2 Confirmation of aromatic amino acids production within boundary
3.4.3 Interaction of groEL1 and groEL2 with △MXAN0049
3.4.4 Significantly produced unknown compounds within boundary
CHAPTER 04 DISCUSSION
4.1 Limitations and
4.2 Future directions
APPENDIX-Ⅰ
List of Abbreviation
List of figures
List of tables
REFERENCES
ACKNOWLEDGEMENT
LIST OF PUBLICATION
学位论文评阅及答辩情况表
本文编号：4029313
【文章页数】：190 页
【学位级别】：博士
【文章目录】：
摘要
Abstract
Chapter 01 INTRODUCTON
1. Overview
1.1 PROTEOMIC
1.1.1 An overview of proteomic approaches
1.1.2 Post-Translation Modifications
1.1.3 Mass Spectrometry-based Proteomics
1.1.4 Database Searching and Protein Identification
1.1.5 Application of proteomics (overview)
1.2 METABOLOMICS
1.2.1 Overview of metabolomics
1.2.2 Advantages of metabolomics
1.2.3 Metabolomics techniques
1.2.4 Applications of metabolomics
1.3 MYXOBACTERIA
1.3.1 Overview of myxobacteria
1.3.2 Diversity and ecology
1.3.3 Myxobacterial genome
1.3.4 Social interactions
1.3.5 Predation
1.3.6 Production of natural products
1.4 COLONY-MERGE INCOMPATIBILITY
1.4.1 Overview of boundary formation
1.4.2 Balance in colony boundaries
1.4.3 Mechanism of colony merging incompatibility
1.5 AIM AND OBJECTIVES
Chapter 02 MATERIAL AND METHODS
2.1 Materials and chemicals
2.1.1 Reagents preparation
2.1.2 Medium and reagents
2.1.3 Apparatus and instruments
2.1.4 Strains and plasmids
2.1.5 List of primers
2.2 Experimental methods
2.2.1 Fluorescence microscopy observation of colony boundaries
2.2.2 Scanning Electron Microscopy (SEM)
2.2.3 Sample preparation for LC-MS/MS
2.2.3.1 Purification of digested proteins and peptides by Zip-Tip
2.2.4 Nano-LC-LTQ-Orbitrap parameters and data processing
2.2.5 Sample preparation and extraction of compounds from boundary
2.2.6 High-resolution HPLC-MS/MS system parameters
2.2.7 T6SS-knockout sample preparation
2.3 Data analysis
Chapter 03 RESULTS
3.1 Role of MXAN-0049 gene in colony boundary formation
3.2 Colony boundaries between incompatible M. xanthus strains under microscope
3.3 Proteomic analysis of colony boundaries
3.3.1 Significantly expressed protein within boundary
3.3.2 Gene ontology of boundary
3.3.3 Significance proteins and their co-relation with boundary formation
3.3.4 Proteomics analysis and KEGG pathways
3.3.5 Role of Protein Export pathway in boundary
3.3.6 Interaction of Cold shock proteinswith RNA degmdation pathway
3.3.7 Co-relationships of boundary formation with T6SS system
3.3.8 Phenylalanine, tyrosine and tryptophan biosynthesis
3.4 Identification of chemical compounds by HPLC-MS/MS
3.4.1 antiSMASH prediction of gene cluster and boundary
3.4.2 Confirmation of aromatic amino acids production within boundary
3.4.3 Interaction of groEL1 and groEL2 with △MXAN0049
3.4.4 Significantly produced unknown compounds within boundary
CHAPTER 04 DISCUSSION
4.1 Limitations and
4.2 Future directions
APPENDIX-Ⅰ
List of Abbreviation
List of figures
List of tables
REFERENCES
ACKNOWLEDGEMENT
LIST OF PUBLICATION
学位论文评阅及答辩情况表
本文编号：4029313
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