Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli

Gerardo Ruiz Amores,Alistair Elfick,Ananda Sanches-Medeiros,Rafael Silva-Rocha,Aitor De Las Heras

doi:10.1038/s41598-017-17114-6

Abstract

Here, we investigated novel interactions of three global regulators of the network that controls biofilm formation in the model bacterium Escherichia coli using computational network analysis, an in vivo reporter assay and physiological validation experiments. We were able to map critical nodes that govern planktonic to biofilm transition and identify 8 new regulatory interactions for CRP, IHF or Fis responsible for the control of the promoters of rpoS, rpoE, flhD, fliA, csgD and yeaJ. Additionally, an in vivo promoter reporter assay and motility analysis revealed a key role for IHF as a repressor of cell motility through the control of FliA sigma factor expression. This investigation of first stage and mature biofilm formation indicates that biofilm structure is strongly affected by IHF and Fis, while CRP seems to provide a fine-tuning mechanism. Taken together, the analysis presented here shows the utility of combining computational and experimental approaches to generate a deeper understanding of the biofilm formation process in bacteria.

Highlights

Bacteria shift from their free-swimming lifestyle to adopt a community structure to benefit from the micro-environment created in a biofilm[1], gaining protection against hazardous substances, and leading in some cases, to antibiotic resistance[1,2,3]
CRP is related to the control of metabolic processes in bacteria and it is differentially activated by substrates[18], while IHF and Fis are dual nucleoid associated proteins (NAPs) that can work both as activators and repressors[19,20]
The resulting network consisted of 37 nodes representing the connections between different transcription factors (TFs), global regulators (GRs) and small molecules (Table S1)

Summary

Escherichia coli

Gerardo Ruiz Amores[1], Aitor de las Heras[2,3], Ananda Sanches-Medeiros[1], Alistair Elfick 2,3 & Rafael Silva-Rocha[1]. An in vivo promoter reporter assay and motility analysis revealed a key role for IHF as a repressor of cell motility through the control of FliA sigma factor expression This investigation of first stage and mature biofilm formation indicates that biofilm structure is strongly affected by IHF and Fis, while CRP seems to provide a fine-tuning mechanism. In Escherichia coli, the complex transcriptional regulatory network of flagella function and curli fimbriae production, the principal biofilm structure indicator, has been investigated in various reports[4,5,6,7] In this organism, the process is controlled by the RpoS sigma factor and FlhDC regulator. The systematic investigation presented here adds new understanding of the complex regulatory program that controls biofilm formation in E. coli, revealing a novel player in this network

Results and Discussion

Conclusions

Author Contributions

Additional Information