Nucleic Acids in the Biofilm Matrix

It has been more than 20 years since 2 the importance of extracellular DNA in biofilm formation was discovered. Since then, the significance of eDNA in bacterial adhesion and biofilm formation has become widely recognized in many bacterial species, and DNA is the only matrix component that almost all biofilms share. eDNA is genomic DNA that originates from bacterial cells or from host immune cells during bacterial infections. It is an important structural component of biofilms, and it provides elasticity to the extracellular matrix, making it capable of stretching and forming streamers in biofilms grown under flow. eDNA interacts with a variety of other biomolecules in the biofilm matrix, including polysaccharides, proteins, and RNA. Importantly eDNA also interacts with itself to form a lattice structure with Holliday Junctions stabilized by DNA-binding proteins. Due to their importance for the biofilm structure, nucleic acids are a prime target for biofilm control. They can be targeted enzymatically with DNases, and RNases can also be effective when used in combination with DNase. In addition to enzymatic degradation, eDNA can also be targeted structurally by removing the DNA-binding proteins that stabilize the DNA lattice. Capturing these proteins with high-affinity antibodies disrupts the biofilm structure. Recent research has shown that DNA’s role in biofilms goes beyond being a structural molecule. eDNA is at the center of extracellular electron transfer via DNA-binding soluble redox-active molecules. This was shown for phenazines in Pseudomonas aeruginosa biofilms. eDNA in biofilms exists in the canonical right-handed B-DNA double helix, it also forms a number of non-canonical secondary structures, of which Z-DNA and G-quadruplex structures are most abundant. Z-DNA is resistant to degradation by DNase I, and it is more mechanically rigid. Z-DNA, therefore, contributes to the biofilm’s resistance to DNase I. G-quadruplex structures are also resistant to DNase I, and these structures can connect multiple strands to form a DNA suprastructure, which increases the biofilm’s elasticity. G-quadruplexes form a complex with hemin which has peroxidase-like catalytic properties. The significance of this DNAzyme activity in the biofilm matrix remains to be investigated. In summary, DNA’s structural versatility makes it a multifunctional component of the extracellular matrix. It provides structural stability, elasticity, protection against enzymatic degradation, transfer of electrons in the extracellular space, and catalysis of chemical reactions. Much still remains to be learned about how bacteria in biofilms harness these properties for their survival.