The Spatial Organization Of Bacterial Transcriptional Regulation Networks

Transcriptional regulation network(TRN)is a directed network constructed according to the regulation relationship between transcription factors(TFs)and their target genes.It is the brain of prokaryotes to receive,process,and response information from inside cell and from the environment.The current research strategies of TRN are mainly focused on network topology and dynamics.However,due to the lack of experimental data,the space distribution of genes and the time required for a TF to find its target gene tend to be ignored when constructing a network dynamic model.As the in vivo movement mechanisms of TF become clearer,it has been found that the strategy for TFs to find their target genes is a scenario integrating diffusion,sliding,hopping and intersegment transfer.The time required for a single TF to find a target gene is far beyond what was previously expected.Previous studies also indicate that the relative position between a TF and its target gene affects the activity and robustness of transcription.Therefore,the spatial structure of bacterial TRN may be optimized during evolution to better fulfill biological function.Recently,the studies of three-dimensional genomes of bacteria such as E.coli and B.subtilis have been published,making it possible to study the features of spatial organization of genome-scale TRN.In this study,we used Escherichia coli and Bacillus subtilis as model species.By integrating TRN data and 3D genome data,the features of spatial organization of TRN were examined from many aspects such as the mode of transcriptional regulation,key nodes of network,hierarchy of network and modules of network.We found that TRNs have a variety of stable spatial organization features under different physiological conditions: 1)contact frequencies between genes with positive regulation relationships are significantly lower than those of genes with negative regulation relationships;2)both Out-Hub nodes and Bottleneck nodes are far away from the nodes which have regulation relationships with them;3)The distances within Middle-Bottom-Target hierarchy in the network have a specific spatial organization pattern;4)the spatial distances of genes in motifs are significantly closer than those of TRN.These results suggest that the spatial structure of bacteria TRN is optimized in multiple levels,which may play an important role in basic bioprocesses of bacteria.