Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis

Abstract

Background: sRNAs, which belong to the non-coding RNA family and range from approximately 50 to 400 nucleotides, serve various important gene regulatory roles. Most are believed to be trans-regulating and function by being complementary to their target mRNAs in order to inhibiting translation by ribosome occlusion. Despite this understanding of their functionality, the global properties associated with regulation by sRNAs are not yet understood. Here we use topological analysis of sRNA targets in terms of protein-protein interaction and transcription-regulatory networks in Escherichia coli to shed light on the global correlation between sRNA regulation and cellular control networks.

Results: The analysis of sRNA targets in terms of their networks showed that some specific network properties could be identified. In protein-protein interaction network, sRNA targets tend to occupy more central positions (higher closeness centrality, p-val = 0.022) and more cliquish (larger clustering coefficient, p-val = 0.037). The targets of the same sRNA tend to form a network module (shorter characteristic path length, p-val = 0.015; larger density, p-val = 0.019; higher in-degree ratio, p-val = 0.009). Using the transcription-regulatory network, sRNA targets tend to be under multiple regulation (higher indegree, p-val = 0.013) and the targets usually are important to the transfer of regulatory signals (higher betweenness, p-val = 0.012). As was found for the protein-protein interaction network, the targets that are regulated by the same sRNA also tend to be closely knit within the transcription-regulatory network (larger density, p-val = 0.036), and inward interactions between them are greater than the outward interactions (higher in-degree ratio, p-val = 0.023). However, after incorporating information on predicted sRNAs and down-stream targets, the results are not as clear-cut, but the overall network modularity is still evident.

Conclusions: Our results indicate that sRNA targeting tends to show a clustering pattern that is similar to the human microRNA regulation associated with protein-protein interaction network that was observed in a previous study. Namely, the sRNA targets show close interaction and forms a closely knit network module for both the protein-protein interaction and the transcription-regulatory networks. Thus, targets of the same sRNA work in a concerted way toward a specific goal. In addition, in the transcription-regulatory network, sRNA targets act as "multiplexor", accepting regulatory control from multiple sources and acting accordingly. Our results indicate that sRNA targeting shows different properties when compared to the proteins that form cellular networks.

Figure 1

sRNA oxyS and its targets in the gene-regulation and protein-protein interaction networks. The dark green lines represent experimentally verified regulation and the dark yellow lines represent predicted regulation. The teal lines indicate indirect regulation (e.g., dinF downstream of lexA in the same operon). Yellow lines are also indirect regulation, but indicate genes of a predicted target. Dashed lines indicate regulated genes extended from an operon structure. Transcription factors under regulation of sRNA have pink borders. Arrow, T, and diamond heads represent positive, negative, and dual regulators, respectively. Circular heads represent predicted, thus unknown, regulation. OxyS regulation deals with multiple stress responses, such as oxidative and osmotic stresses.