THE SUBTLE BIOFILM REGULATION IN ESCHERICHIA COLI: CSGD AND THE YDDV-DOS OPERON

In this PhD thesis work I investigated the expression modulation of the major adhesion factors in Escherichia coli; in particular I focused on the role of GGDEF and EAL proteins, on their modulation in E. coli biofilm formation in response to environmental signals and on regulation of curli fibers, cellulose and poly-N-acetylglucosamine (PNAG), the most important biofilm determinants in E. coli. E. coli is an Enterobacterium, normally living inside the mammalian gut, at temperature of 37° C and in relatively nutrient-rich environment. Once outside the host, bacteria usually face much lower temperatures (< 30°C) and a nutrient-limiting environment. The biofilm determinants studied in this thesis are all expressed in response to environmental conditions such as low temperature, low osmolarity and starvation, suggesting that E. coli bacteria switch to a biofilm mode of growth as part of their adaptation to the natural environment. In response to reduction in growth rates, E. coli seems to canalize its energy consumption into production of extracellular features such as curli or exopolysaccharides. Biofilms can be thus considered as a “resistance form” of growth able to withstand stress conditions more efficiently than cells living in a planktonic mode of growth. The CsgD protein is the master regulator of E. coli biofilm formation. It is a transcriptional factor necessary for curli genes transcription and, through the AdrA protein, for cellulose biosynthesis. Gene regulation by CsgD is tightly connected to production and sensing of cyclic di-GMP, a bacterial second messenger involved in various cellular processes, including biosynthesis of extracellular polysaccharides (Simm et al., 2004), biofilm formation (Hickman et al., 2005), and virulence (Pratt et al., 2007; Tischler and Camilli, 2005), as well as morphological and physiological differentiation (Paul et al., 2004). The CsgD-dependent adrA gene, involved in cellulose biosynthesis (Zogaj et al., 2001), encodes a cyclic di-GMP synthase (Simm et al., 2004). CsgD can also activate yoaD, whose gene product is a cyclic di-GMP phosphodiesterase, suggesting that CsgD is directly involved in feedback regulation of cyclic di-GMP intracellular levels and of cellulose biosynthesis (Brombacher et al., 2006). CsgD is also able to activate the iraP gene: IraP acts as a stabilization factor for the σs protein, an alternative sigma factor of RNA polymerase which directs transcription of genes involved in adaptation to slow growth and to cellular stresses. Here I showed that CsgD transcription activation of the iraP gene does result in a significant increase of σs intracellular concentration by positively affecting σs protein stability, thus leading to altered expression of σs-dependent genes. CsgD-mediated increase of σs cellular concentrations via the iraP gene would trigger an autoactivation loop leading to an increased production of CsgD-dependent adhesion determinants such as curli fibers and cellulose. This autoregulatory circuitry might be further fueled by σs-dependent induction of genes encoding di-guanylate cyclases, i.e., proteins able to synthesize the second messenger di-cyclic- GMP, which, in turn, can positively affect csg gene expression (Kader et al., 2006; Weber et al., 2002). The yddV-dos operon is the most expressed among c-di-GMP-related genes showing dependence on σs (Weber et al., 2006; Sommerfeldt et al., 2009). It encodes, respectively, a protein with DGC activity and a PDE that can degrade c-di- GMP to pGpG. Both Dos and YddV are heme-binding oxygen sensors, and interact to form a stable protein complex (Tuckerman et al., 2009). Although it has been reported that YddV overexpression can stimulate biofilm formation (Mendez-Ortiz et al., 2006), the targets of yddV-dependent biofilm induction had not yet been identified. Here I showed that YddV acts modulating curli and PNAG expression. Control of curli production by yddV-dos takes place at the level of transcription regulation of the csgBAC operon, encoding curli structural subunits, and is mediated by the DGC and PDE activities of YddV and Dos. In contrast, the YddV–Dos protein complex does not strongly influence csgDEFG expression, nor does it affect the expression of the CsgD-dependent adrA gene, encoding a positive effector for cellulose biosynthesis. Regarding PNAG production, we showed that YddV is able to prevent degradation of pgaABCD transcript in the MG1655csrA background, thus suggesting that a DGC might regulate gene expression by affecting mRNA stability in E. coli. YddV regulation of pgaABCD operon in a wild type contest is still controversial: pgaABCD genes are expressed at low levels in MG1655 (the standard laboratory strain of E. coli) and their mRNA half-life is lower than two minutes regardless of the growth conditions tested; thus, possible effects of yddV inactivation on destabilization of the pga transcript are not easy to evaluate in the wt contest. In the last part of my thesis I tried to characterize a biofilm-forming mutant of E. coli, able to express pgaABCD genes at high levels. Even if initial data suggested that a mutation in the csrA gene could be responsible for pga mRNA stabilization in this mutant, actual the mutation leading to the adhesive phenotype and to PNAG production is outside the csrA gene and is still unknown. Moreover my data suggest a connection between pga expression and iron regulation in E. coli strains: it is conceivable that pgaABCD expression and consequent biofilm formation and the adherent phenotype depends on concerted production of different determinants, whose expression is also affected by iron concentration. Thus, my research highlighted that biofilm production is the result of coordinated expression of different adhesion determinants, whose regulation is complex and not fully understood. In particular, the precise extent and the molecular mechanism of c-di-GMP adhesion factors regulation remains to be largely identified and represents an exciting challenge for future research in the biofilm field.