Bacterial "life-style" choices: Coordination of motility and biofilms functions by GGDEF/EAL proteins in Escherichia coli
Final Report Abstract
Most bacteria can switch between the motile/planktonic and sedentary/multicellular "life-styles". The latter represents bacterial biofilms characterized by the production of an extracellular polymeric matrix, which in E. coli K-12 consists essentially of amyloid curli fibres. In the first funding period of this project we showed that in E. coli motility and curli production are inversely coordinated by multiple factors that include the general stress sigma factor sigma s, the sigma s-antagonist FliZ, various GGDEF/EAL proteins and a group of novel small regulatory proteins. Most GGDEF and EAL domains exhibit diguanylate cyclase (DGC) and phosphodiesterase (PDE) activities, respectively, and thereby control the ubiquitous bacterial second messenger c-di-GMP. All these components are tightly integrated in a complex regulatory network, which converges in the control of expression and activity of CsgD, which emerged as a highly signal-integratory and decisive master regulator for entering into and shaping the sedentary/multicellular existence of E.coli and related bacteria. In the second period of this project (2009-2012), the overall goal was to sharpen several key concepts and to work out the functional details of this network at the molecular level. Research focussed on three major aspects: (i) FliZ, which was demonstrated to be a novel type of abundant nucleoid-associated protein with a DNA-binding specificity overlapping sigma s-dependent promoter sequences that eventually gets degraded, was found to act as a timing factor for the motility-to-curli production switch (giving motility priority over sigma s-dependent functions by competing for promoter binding with sigma s-RNA polymerase); (ii) a cascade of two c-di-GMP control modules each consisting of a DGC/PDE pair - YegE/YhjH and YdaM/YciR - was demonstrated to regulate the expression of the curli activator gene csgD via controlling the activity of the transcription factor MlrA; moreover, YciR, YdaM and MlrA directly interact with each other, indicating local c-di-GMP signalling with the PDE YciR acting as a 'trigger enzyme'; (iii) as an example of a 'degenerate' EAL domain protein, the role of the unorthodox EAL protein YcgF (now termed BluF) was elucidated: BluF directly binds and antagonizes the repressor YcgE (now termed BluR), resulting in expression of a series of small regulatory proteins (YcgZ, YmgA, YmgB, YmgC) that down-regulate CsgD and curli expression by activating the Rcs phosphorelay system. Overall, by elucidating the central role of CsgD and its upstream regulatory network that uses several paradigmatic c-di-GMP control modules, this project has made a major step forward in our understanding of c-di-GMP signaling in general and has set the stage to address the role of all 12 DGCs and 13 PDEs in biofilm formation and potentially additional functions in E. coli.
Publications
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(2009) Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli. Microbiology 155, 1318-1331
Sommerfeldt, N., A. Possling, N. Tschowri, G. Becker, C. Pesavento, H. Weber, and R. Hengge
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(2009) Nucleotide-based second messengers in bacteria. Curr. Op. Microbiol. 12, 170-176
Pesavento, C., and R. Hengge
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(2009) Principles of cyclic-di-GMP signaling. Nature Rev. Microbiol. 7, 263-273
Hengge, R.
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(2009) The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue light stress response of E.coli. Genes Dev. 23, 522-534
Tschowri, N., S. Busse, and R. Hengge
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(2010) Cyclic-di-GMP reaches out into the bacterial RNA world. Science Signal. 3, pe44
Hengge, R.
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(2010) Cyclic-di-GMP signaling. In: Bacterial Signaling (eds. K. Jung and R. Kraemer), Wiley VHC, pp. 377-394
Pesavento, C. and R. Hengge
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(2010) The role of c-di-GMP in the regulatory networks of Escherichia coli. In: The Second Messenger Cyclic Di-GMP (eds. K. Visick and A. Wolfe), ASM Press, Washington, D.C., pp. 230-252
Hengge, R.
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(2012) Molecular function and potential evolution of the biofilm-modulating blue light-signaling pathway of Escherichia col. Mol. Microbiol. 85, 893-906
Tschowri, N., and R. Hengge
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(2012) The global repressor FliZ antagonizes gene expression by σS–containing RNA polymerase due to overlapping DNA binding specificity. Nucl. Acids Res. 40, 4783-4793
Pesavento, C., and R. Hengge
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2012. Targeting of csgD by the small regulatory RNA RprA links stationary phase, biofilm formation and cell envelope stress in Escherichia coli. Mol. Microbiol. 84:51-65
Mika, F., S. Busse, A. Possling, J. Berkholz, N. Tschowri, N. Sommerfeldt, M. Pruteanu, and R. Hengge
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(2013) The EAL protein YciR is a trigger enzyme in a c-di-GMP signaling cascade in E. coli biofilm control. EMBO J. 32, 2001-2014
Lindenberg, S., G. Klauck, C. Pesavento, H. Weber, E. Klauck, and R. Hengge
