SPP 1879: Sensory Mechanisms of c-di-GMP Signaling in E. coli Biofilm Formation


Bacterial biofilms colonize diverse surfaces and are highly resistant against antibiotics or host immune systems. In these biofilms, cells are embedded in a self-produced protective matrix of extracellular biopolymers. Major biofilm matrix components in E. coli are amyloid curli fibres and the exopolysaccharide cellulose whose synthesis is under control of the stationary phase sigma factor RpoS (σS) and the second messenger c-di-GMP. The latter is produced by diguanylate cyclases (DGC, with GGDEF domains) and is degraded by specific phosphodiesterases (PDE, with EAL domains). 25 of the 29 GGDEF/EAL domain proteins of E. coli K-12 are enzymatically active, with 12 being DGCs and 13 being PDEs. Many of these differentially expressed DGCs and PDEs are membrane-associated and their activities are controlled by N-terminal sensory domains. Using biofilm matrix production as a c-di-GMP target that provides for convenient phenotypes and readouts for genetic, molecular biological and biochemical analyses, the proposed project aims at clarifying the molecular mechanisms of signal sensing and processing at the primary and secondary levels of c-di-GMP signaling in E. coli. This includes (i) sensing environmental and cellular signals via the N-terminal sensory input domains of a novel class of PDEs, and (ii) sensing c-di-GMP via novel and unorthodox c-di-GMP effector mechanisms.
In particular, the following signal perception and c-di-GMP effector mechanisms will be studied:
• Redox control of cytoplasmic enzyme activity via disulfide bond formation and proteolytic processing in the periplasmic loop domain of the six E. coli PDEs with CSS-EAL domain architecture
• Molecular structure, function and targets of YbjK, a DeoR-like transcription factor that seems to bind c-di-GMP as a G-quadruplex
• Regulation of transcription by PdeL, a locally acting c-di-GMP-binding and -degrading 'trigger PDE' and transcription factor with a LuxR-EAL domain architecture
• Structure and function of a putative c-di-GMP riboswitch in the intergenetic region of the mRNA of the orf0317-pdeL operon, which down-regulates PdeL expression.
Furthermore, the integration of these molecular processes within the large regulatory network that controls matrix production and thereby generates functionality and architecture of a biofilm will be elucidated. With its focus on sensory input in the control of DGCs and PDEs, c-di-GMP-sensing effector components and local c-di-GMP signalling, this project is expected to make a major contribution to achieving the goals of SPP 1879. Moreover, its results will have practical applications, e.g. in the development of novel anti-biofilm strategies or in synthetic biology.

Principal Investigators
Hengge, Regine Prof. Dr. (Details) (Microbiology)

Duration of Project
Start date: 09/2016
End date: 02/2020

Research Areas
Microbiology, Virology and Immunology

Publications
Original Research Publications

Sarenko, O., G. Klauck, F.M. Wilke, V. Pfiffer, A.M. Richter, S. Herbst, V. Kaever, and R. Hengge (2017) More than enzymes that make and break c-di-GMP - the protein interaction network of GGDEF/EAL domain proteins of Escherichia coli. mBio 8: e01639-17. doi: 10.1128/mBio.01639-17.

Thongsomboon, W., D.O. Serra, A. Possling, C. Hadjineophytou, R. Hengge and L. Cegelski (2018) Phosphoethanolamine cellulose: a naturally produced chemically modified cellulose. Science 359: 334-338. doi: 10.1126/science.aao4096.

Herbst, S., M. Lorkowski, O. Sarenko, T.K.L. Nguyen, T. Jaenicke, and R. Hengge (2018) Transmembrane redox control and proteolysis of PdeC, a novel type of c-di-GMP phosphodiesterase. EMBO J. 37: e97825 (published ahead of print on Apr 13). doi: 10.15252/embj.201797825.

Serra, D.O., and R. Hengge (2019) A c-di-GMP-based switch controls local heterogeneity of extracellular matrix synthesis which is crucial for integrity and morphogenesis of Escherichia coli macrocolony biofilms. J. Mol. Biol.431: 4775-4793. doi: 10.1016/j.jmb.2019.04.001.

Pfiffer, V., O. Sarenko, and R. Hengge (2019) Genetic dissection of E. coli´s master diguanylate cyclase DgcE: role of the N-terminal MASE1 domain and direct signal input from a GTPase partner system. PLoS Genetics 15: e1008059. doi: 10.1371/journal.pgen.1008059.

Kettles, R., N. Tschowri, , K. Lyons, P. Sharma, R. Hengge, M. Webber, and D. Grainger (2019) The Escherichia coli MarA protein regulates the ycgZ-ymgABC operon to inhibit bioiflm formation. Mol. Microbiol. 112: 1609-1625. doi: 10.1111/mmi.14386.

Reviews

Hengge. R. (2016) Trigger phosphodiesterases as a novel class of c-di-GMP effector proteins. Philos. Trans. R. Soc. Lond. B 371: 20150498. doi: 10.1098/rstb.2015.0498.

Serra, D.O., and R. Hengge (2017) Experimental detection and visualization of the extracellular matrix in macrocolony biofilms. Methods Mol. Biol. 1657: 133-145. doi: 10.1007/978-1-4939-7240-1_11.

Hengge, R., S. Häussler, M. Pruteanu, J. Stülke, N. Tschowri, and K. Turgay (2019) Recent advances and current trends in nucleotide second messenger signaling in bacteria. J. Mol. Biol. 431: 908-927. doi: 10.1016/j.jmb.2019.01.014.

Book Chapters

Serra, D.O., and R. Hengge (2017) Experimental detection and visualization of the extracellular matrix in macrocolony biofilms. In c-di-GMP Signaling: Methods & Protocols - Methods in Molecular Biology (Sauer, K., ed.), Humana Press, Springer Nature, New York, N.Y., pp. 133-145. doi.org/10.1007/978-3-030-12919-4_8.
Link: https://link.springer.com/chapter/10.1007/978-3-030-12919-4_8

Serra, D.O., and R. Hengge (2019) Cellulose in bacterial biofilms. In Extracellular Sugar-Based Biopolymer Matrices (Cohen, E., and Merzendorfer, H., eds.). Biologically-Inspired Systems, vol. 12, Springer, pp. 355-392. doi.org/10.1007/978-3-030-12919-4_8.

Hengge, R. (2019) Durch den Datendschungel auf der Suche nach Erkenntnis: Experimentieren in der molekularen Mikrobiologie. In Experimentieren.Vergleich experimenteller Kulturen in Wissenschaft und Gestaltung (Marguin, S., H. Rabe, W. Schäffner, F. Schmidgal (eds), Transcript-Verlag, Bielefeld.

Last updated on 2021-04-01 at 17:44