The Spatial Organization of Bacterial Transcriptional Regulatory Networks

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...

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Bibliographic Details
Published in:Microorganisms (Basel) 2022-11, Vol.10 (12), p.2366
Main Authors: Tian, Liu, Liu, Tong, Hua, Kang-Jian, Hu, Xiao-Pan, Ma, Bin-Guang
Format: Article
Language:English
Subjects:
3D genome
Bacillus subtilis
Bacteria
bacterial chromatin
Chromatin
Chromosomes
Circuit design
Coliforms
Datasets
E coli
Environmental information
Escherichia coli
Gene regulation
Genes
Genetic aspects
Genetic transcription
Gram-positive bacteria
Microbiological research
network hierarchy
network motif
Proteins
RNA polymerase
spatial effect
Transcription
Transcription factors
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Summary: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 and have been published, making it possible to study the spatial organization of bacterial transcriptional regulatory networks. By combining TRNs and chromatin interaction data of and , 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.
ISSN:2076-2607
2076-2607
DOI:10.3390/microorganisms10122366