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

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.

Trouble is coming: Signaling pathways that regulate general stress responses in bacteria

“…cAMP is synthesized when the cell is using secondary carbon sources (rather than glucose), and the global transcriptional regulator CRP, in complex with cAMP, positively regulates the genes necessary for using these less-favored carbon sources. A number of studies show higher levels of RpoS early in exponential phase in the absence of cAMP and CRP (3,17,23,24), suggesting negative transcriptional regulation by CRP/cAMP, and based on these studies, EcoCyc currently shows the rpoS promoter as negatively regulated by CRP (25). However, other studies show positive effects of cAMP and CRP (26), and muta- JBC REVIEWS: Bacterial general stress responses tions in the suggested CRP-binding sites upstream and downstream of the major rpoS promoter significantly reduced RpoS expression (23), providing compelling evidence for an important positive role for CRP for RpoS transcription.…”

“…Other regulators, including Fis and the antitoxin MqsA, have also been implicated in transcriptional regulation of rpoS (24,28). Fis is an abundant nucleoid-associated protein; in a recent study, mutations in fis increased expression of an rpoS transcriptional fusion, and possible sites for Fis binding were identified by sequence comparisons.…”

“…Fis is an abundant nucleoid-associated protein; in a recent study, mutations in fis increased expression of an rpoS transcriptional fusion, and possible sites for Fis binding were identified by sequence comparisons. This fusion contains the full leader, leaving open the possibility of a more indirect effect of Fis (24,29). The physiological implications of this regulation have not been explored.…”

Evolution of Honey Resistance in Experimental Populations of Bacteria Depends on the Type of Honey, and Has no Major Side Effects for Antibiotic Susceptibility

“…Biofilm formation is an effective bacterial defense mechanism against a wide range of antimicrobials (Costerton et al, 1995). Several of the genes we found mutated in honey-adapted isolates have a known role in biofilm formation (fimA, fimE, nlpD, ompR, yeaJ (Prigent-Combaret et al, 2001;Niba et al, 2007;Wu and Outten, 2009;Amores et al, 2017)). Honey or honey-resistance mechanisms might therefore also have downstream effects for biofilm formation or the expression of other virulence factors.…”

Evaluation of Acquired Antibiotic Resistance in Escherichia coli Exposed to Long-Term Low-Shear Modeled Microgravity and Background Antibiotic Exposure

“…categorized as an essential gene for E. coli Flanking genes encode metabolite transport proteins Mutation is in the 3rd base upstream of the start codon "ATG" of the fimA gene marR ¡ (intragenic) Multidrug resistance (81) E131V is in the DNA-binding domain involved in organic solvent tolerance 88 Highly conserved in Gram-negative bacteria; encodes the thin, coiled aggregative surface filaments called curli (curli mediate adhesion [135][136][137][138] and wound colonization and interaction with the immune system [138,139] and influence stress responses, quorum sensing [140], and biofilms [141] and resistance to gentamicin [54] and control ASR genes [142,143] 14-gene cluster, central to chemotaxis and biofilm formation (144,147); cheR, cheW (chemotaxis), and motA (motility) are considered essential for E. coli (129) Loss of gene cluster potentially results in a fitness cost of antibiotic resistance in 1000-BA the bioburden of microbes in the confined spaces of manned space flight missions. This is most likely to happen independently of the microgravity component.…”