Regulation of curli gene expression in Escherichia coli

Under stressful conditions, bacteria produce extracellular matrix for long-term survival. Curli fibers are the key proteinaceous component of such matrix produced by E. coli and other enteric bacteria. Curli-rich matrix encapsulates individual cells, promoting cell-to-cell interactions and contributing to the cell survival under multiple harsh conditions. Structural components and assembly factors of curli are encoded by two operons, csgBAC and csgDEFG, with the csgD gene controling transcription of both operons. Expression of curli fibers responds to multiple environmental signals and is heavily regulated on transcriptional and post-transcriptional levels. The csg intergenic region is a hub for signal integration and is under regulation of a variety of transcriptional factors, second messenger c-di-GMP and a number of small RNAs. Curli gene expression is induced only in a subpopulation of bacteria, leading to heterogeneity of extracellular matrix synthesis. Although many genetic determinants modulating curli production in biofilms are known, there is a lack of knowledge about regulation of curli gene expression in unstructured planktonic cultures. Furthermore, the origin of heterogeneous curli expression still remains unknown. Here, with the help of a gene knock-out approach combined with flow cytometry and plate reader analyses a systematic investigation of the role of c-di-GMP network and multiple cell factors in expression of curli structural genes was performed. Bimodal activation of curli expression was found to occur not only in submerged and macrocolony biofilms, but also in unstructured planktonic cultures of E. coli, resulting in stochastic differentiation into distinct subpopulations of curli-positive and curli-negative cells at the entry into the stationary phase of growth. Multiple regulators involved in regulation of stress response, cell motility, cell physiology and metabolism, as well as in formation of extracellular matrix and maintenance of DNA architecture were found to modulate expression of curli by either promoting or repressing activity of the csgBA genes. Regulators which act upstream of the master transcription factor CsgD and which are crucial for bimodality of curli gene expression were further elucidated. The impact of the PdeH/DgcE/PdeR/DgcM signaling pathway as well as individual diguanylate cyclases on the regulation of the csgBA activity was determined. The c-di-GMP regulatory network was found to modulate csgBA expression levels and to increase robustness of curli expresion to environmental variation, while not required for the emergence of bimodal curli gene expression in E. coli. Overall, this study provides an overview of regulation of curli gene expression in planktonic E. coli culture in the absence of any microenvironmental gradients.