Insights on Escherichia coli biofilm formation and inhibition from whole-transcriptome profiling

Abstract

Biofilms transform independent cells into specialized cell communities. Here are presented some insights into biofilm formation ascertained with the best-characterized strain, Escherichia coli. Investigations of biofilm formation and inhibition with this strain using whole-transcriptome profiling coupled to phenotypic assays, in vivo DNA binding studies and isogenic mutants have led to discoveries related to the role of stress, to the role of intra- and interspecies cell signalling, to the impact of the environment on cell signalling, to biofilm inhibition by manipulating cell signalling, to the role of toxin/antitoxin genes in biofilm formation, and to the role of small RNAs on biofilm formation and dispersal. Hence, E. coli is an excellent resource for determining paradigms in biofilm formation and biofilm inhibition.

Fig. 1

E. coli BW25113 biofilm as viewed using the green-fluorescent-protein-expressing plasmid pCM18, confocal microscopy, and IMARIS software (conditions: Luria broth after 48 hr at 37°C, flow rate of 10 mL/hr). Scale bar (upper right) indicates 10 μm.

Fig. 2

Schematic of E. coli proteins related to biofilm formation. Proteins that were identified through whole-transcriptome studies and later characterized as described in this review are shown in red.

Fig. 3

Structure of biofilm-related compounds: cyclic diguanylic acid (c-di-GMP), N-butyryl-L-homoserine lactone (C4HSL), 4,5-dihydroxy-2,3-pentanedione (DPD), 7-hydroxyindole, isatin, (5Z)-4-bromo-5-(bromomethylene)-3-butyl-2(5H)-furanone (furanone), palmitic acid, ursolic acid, and asiatic acid.

Fig. 4

Structure of AriR (YmgB) dimer (Lee et al., 2007c). AriR forms a dimer in solution, as determined using size exclusion chromatography and was crystallized as a head-to-head dimer. The final model includes two protein molecules (each containing residues 25–86) and 31 water molecules; the N-terminal 24 amino acids of AriR are spontaneously cleaved. Each subunit of the AriR dimer consists of three α-helices, spanning residues 27–44 (α1), 50–62 (α2) and 67–84 (α3). Helices α2 and α3 are oriented in a near perfect anti-parallel fashion with respect to one another with helix α1 crossing in front of them at nearly a 90° angle. The tertiary structure of the monomer is maintained by an extensive network of hydrophobic interactions consisting almost exclusively of leucine, isoleucine, and valine residues. The peripheral residues of the protein are primarily polar and charged. The dimerization contact is mediated predominantly by residues in helix α1, including Ser31, Leu34, Gly35, Val38, Thr39, Val48, and Met42, and results in the burial of 1326 Ų of solvent accessible surface. Like AriR, Hha is an all α-helical protein although it has four helices while AriR has three.

Fig. 5

CsrA regulatory protein and sRNA CsrB which binds CsrA (Babitzke and Romeo, 2007). Secondary structure of sRNA CsrB showing 22 GGA regions for binding CsrA proteins (a). CsrA consensus binding sequence (b). Structure of CsrA dimer with possible CsrB binding residues shown.