在Vibrio natriegens的系统生物学能力通过将新型数据分析应用于转录基因组来揭示
Jongoh Shin1, Kevin Rychel1, Bernhard O Palsson2
1Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.
Cell reports
|June 7, 2023
概括
维布里奥纳特里根的自然能力是由特定的基因组调节的,称为iModulons. 机器学习确定了参与DNA吸收的关键iModulons,揭示了能力和基本细胞功能之间的联系.
科学领域:
- 微生物学 微生物学
- 系统生物学 系统生物学
- 基因组学就是基因组学.
背景情况:
- 对于DNA吸收至关重要的Vibrio natriegens自然能力,部分通过TfoX和QstR转录因子来理解.
- 管理能力的完整的遗传和转录监管网络在很大程度上是未知的.
研究的目的:
- 为了全面阐明Vibrio natriegens.中的自然能力的转录组调节基础.
- 识别控制能力的新型基因调控模块 (iModulons) 以及它们与管理功能的关系.
主要方法:
- 应用了机器学习方法,将Vibrio natriegens转录组分解为45个独立调节的基因组 (iModulons).
- 对83种基因删除菌株进行了表型查,以评估对能力的影响.
- 集成的转录基因组数据与功能基因组学,以建立监管关系.
主要成果:
- 对Vibrio natriegens的能力与抑制铁代谢和翻译iModulons以及激活六个iModulons有关.
- 确定了TfoX,QstR,一种新型的iModulon和iModulons作为关键调节者,用于运动性,多聚化和反应性氧物种 (ROS) 反应.
- 已识别的iModulons中的功能丧失显著减少或取消了自然能力.
结论:
- 这项研究揭示了Vibrio natriegens自然能力背后的转录结构.
- 建立了一个新的数据库-iModulon-发现周期,以了解复杂的生物过程.
- 提供了基础的遗传和系统层面的理解,用于未来对Vibrio natriegens能力的研究.
相关概念视频
Synthetic Biology
4.9K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
4.9K
Gene Regulation in Microbial Communities: Quorum Sensing
51
Quorum sensing is a mechanism of bacterial communication that enables coordinated gene expression in response to changes in population density. This facilitates collective behaviors that enhance survival, resource acquisition, and ecological adaptation. This process relies on small signaling molecules called autoinducers that accumulate as bacterial populations grow. When a critical threshold concentration of autoinducers is reached, bacterial cells collectively modify gene expression,...
51
Modern Molecular Taxonomy
56
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
56
Applications of Molecular Taxonomy
42
Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
42
Coordination of Gene Expression Processes in Bacteria
44
The DNA replication, transcription, and translation processes are intricately coupled in bacteria, allowing efficient gene expression and rapid protein synthesis. While this physical and functional coordination is advantageous, it introduces challenges that bacteria overcome through specific regulatory mechanisms.Coupling of Replication, Transcription, and TranslationThe coupling of replication, transcription, and translation is a hallmark of bacterial gene expression. As the replisome unwinds...
44
Riboswitches
8.2K
Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
8.2K


