Key Molecular Mechanisms of c-di-GMP Signaling in Bacterial Biofilm Formation
Final Report Abstract
The molecular mechanisms underlying bacterial biofilm formation are being studied intensively because biofilms – in which bacteria are well protected against antibiotics and the attacks of host immune systems – are causally involved in most chronic infections. Biofilm formation, i.e. the production of a protective extracellular matrix and other biofilm-associated components, is nearly ubiquitously promoted by the second messenger c-di-GMP. This signaling molecule is produced by diguanylate cyclases (DGC) and degraded by specific phosphodiesterases (PDE), whose activity is controlled by a variety of N-terminal sensory input domains. Most bacterial species possess multiples of these enzyme, which often have surprisingly specific functions. Thus, E. coli K-12 has 12 DGCs and 13 PDEs, which are nearly all expressed in parallel, yet specific ones control distinct biofilm-associated functions. The project focused on two key aspects of c-di-GMP signaling in the model bacterium Escherichia coli: (1) Local c-di-GMP signaling involving protein-protein interactions of specific c-di-GMP-related enzymes with cognate effector/target proteins and the concept of trigger PDEs, which play a central role these signaling protein complexes; and (2) sensory input into c-di-GMP signaling with the goal of characterizing the molecular mechanisms of signal perception and processing by N-terminal sensory domains of the enzymes that make or break c-di-GMP. The theoretical concept and molecular functioning of trigger PDEs as a novel class of c-di-GMP sensing effector proteins was worked out using PdeR as an example, which is the key component in a larger local c-di-GMP signaling protein complex that is crucial for controlling the expression of CsgD, the major matrix regulator in E. coli. The results also led to a novel model of local c-di-GMP signaling, in which a master PDE (PdeH in E. coli) maintains a very low global c-di-GMP level by eradicating the contributions of many DGCs, whose c-di-GMP production is thus allowed to specifically control directly contacted effector/target systems without changing the global cellular c-di-GMP pool. A comprehensive pangenome-based catalog of the DGCs and PDEs of E. coli and their diverse sensory input domains was established and two particularly interesting novel signal input pathways were characterized in molecular detail: (1) the redox control of cytoplasmic PDE activity by the periplasmic-transmembrane CSS domains found in five CSS domain PDEs of E. coli; and (2) the role of the transmembrane MASE1 domain and an interacting GTP-sensing GTPase partner system (RdcA/B) in activating DgcE, the master DGC in the control of biofilm matrix production by E. coli. These new insights in the molecular mechanisms of the major players in c-di-GMP signaling have been integrated into the large regulatory network that generates the complex microarchitecture and functionality of E. coli biofilms. Thereby, this project has also generated novel perspectives on the development of urgently needed anti-biofilm strategies and agents.
Publications
- (2015) Logical-continuous modelling of post-translationally regulated bistability of curli fiber expression in Escherichia coli. BMC Syst. Biol. 23, 39
Yousef, K.P., A. Streck, C. Schütte, H. Siebert, R. Hengge, and M. von Kleist
(See online at https://doi.org/10.1186/s12918-015-0183-x) - (2016) Genome-based comparison of c-di-GMP signaling in pathogenic and commensal Escherichia coli strains. J. Bacteriol. 198: 111-126
Povolotsky, T.L., and R. Hengge
(See online at https://doi.org/10.1128/JB.00520-15) - (2016) Trigger phosphodiesterases as a novel class of c-di-GMP effector proteins. Philos. Trans. R. Soc. Lond. B 371: 20150498
Hengge, R.
(See online at https://doi.org/10.1098/rstb.2015.0498) - (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
Sarenko, O., G. Klauck, F.M. Wilke, V. Pfiffer, A.M. Richter, S. Herbst, V. Kaever, and R. Hengge
(See online at https://doi.org/10.1128/mBio.01639-17) - (2018) Transmembrane redox control and proteolysis of PdeC, a novel type of c-di-GMP phosphodiesterase. EMBO J. 37: e97825
Herbst, S., M. Lorkowski, O. Sarenko, T.K.L. Nguyen, T. Jaenicke, and R. Hengge
(See online at https://doi.org/10.15252/embj.201797825) - (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
Pfiffer, V., O. Sarenko, and R. Hengge
(See online at https://doi.org/10.1371/journal.pgen.1008059)
