The Spatial Organization of Bacterial Transcriptional Regulatory Networks.
Liu TianTong LiuKang-Jian HuaXiao-Pan HuBin-Guang MaPublished in: Microorganisms (2022)
The transcriptional regulatory network (TRN) is the central pivot of a prokaryotic organism to receive, process and respond to internal and external environmental information. However, little is known about its spatial organization so far. In recent years, chromatin interaction data of bacteria such as Escherichia coli and Bacillus subtilis have been published, making it possible to study the spatial organization of bacterial transcriptional regulatory networks. By combining TRNs and chromatin interaction data of E. coli and B. subtilis , we explored the spatial organization characteristics of bacterial TRNs in many aspects such as regulation directions (positive and negative), central nodes (hubs, bottlenecks), hierarchical levels (top, middle, bottom) and network motifs (feed-forward loops and single input modules) of the TRNs and found that the bacterial TRNs have a variety of stable spatial organization features under different physiological conditions that may be closely related with biological functions. Our findings provided new insights into the connection between transcriptional regulation and the spatial organization of chromosome in bacteria and might serve as a factual foundation for trying spatial-distance-based gene circuit design in synthetic biology.
Keyphrases
- transcription factor
- escherichia coli
- gene expression
- dna damage
- bacillus subtilis
- squamous cell carcinoma
- electronic health record
- systematic review
- healthcare
- dna methylation
- copy number
- machine learning
- lymph node
- candida albicans
- risk assessment
- deep learning
- sentinel lymph node
- oxidative stress
- social media
- network analysis
- biofilm formation
- cystic fibrosis
- multidrug resistant