Molecule of the Month: Biofilms

When you think of bacteria, you might imagine individual cells swimming freely in water or growing on a laboratory dish. In reality, many bacteria prefer a very different lifestyle. When they find an appropriate surface, which could be a rock, a tooth, or a metal surface, bacteria tend to settle down, multiply, and wrap themselves in a glue-like material, forming a biofilm. The self-made extracellular matrix, a coating of secreted sugars, proteins, and DNA, acts as a protective layer that anchors bacteria in place while shielding them from dehydration as well as from disinfectants and antibiotics. Although many biofilms are harmless or even beneficial, they can also create serious problems when they develop in places where bacteria are unwanted.

One significant challenge posed by biofilms is in food safety. Food processing equipment, such as conveyor belts, storage containers, and cutting surfaces can all provide surfaces where bacteria attach and establish biofilms. Once established, these microbial communities become much more difficult to remove than individual bacteria. Even after routine cleaning and sanitizing, biofilms can persist in tiny cracks and hard-to-reach areas, periodically releasing bacteria that contaminate food products. This contributes to product recalls and outbreaks of foodborne illness caused by pathogens such as Listeria monocytogenes, Salmonella enterica, and some strains of Escherichia coli.

In medicine, biofilms are responsible for many chronic and difficult-to-treat infections. They can develop on catheters, heart valves, and other implanted medical devices. Because bacteria within biofilms in the body can be highly resistant to antimicrobial treatments and the immune system, infections often become persistent and require prolonged treatment.

Understanding the components of biofilms and the molecular machinery bacteria use to produce them can enable new strategies that prevent biofilm formation or break apart existing biofilms. Importantly, these efforts can lead to improvements in food safety, reductions in healthcare-associated infections, and help preserve the effectiveness of antibiotics in the fight against antimicrobial resistance.

A majority of a biofilm's mass is not cells, but the polymers of sugars, proteins, and DNA that are secreted by them. Some bacteria, including E. coli and Salmonella, produce long filaments of cellulose, the same glucose polymer that stiffens plant cell walls, to form a tough mesh network. The enzyme responsible is the cellulose synthase complex, BcsA–BcsB (shown on the right, pdb_00004p00 and pdb_00009b8v), a multi-protein complex embedded in the bacterial inner membrane. BcsA (shown in purple) adds one glucose at a time from UDP-glucose and feeds the growing sugar chain (shown in yellow) through a channel in its inner membrane-spanning domain. It is aided by six copies of BcsB, which form a semicircular structure above BcsA.

BcsA-BcsB activity is controlled by a small molecule of cyclic di-GMP, a master second messenger that governs a bacterium's choice between roaming free or settling into a biofilm. Binding of cyclic di-GMP releases a previously tethered protein loop and opens the door for substrate (take a closer look at this switch in the Exploring the Structure section). The same cyclic di-GMP signal also ramps up production of other adhesive molecules, including the production of sticky strands of curli proteins, described below, and stops the bacterium from swimming by turning off flagellar activity. BcsA activity is also regulated by its interaction with BcsE (pdb_00006ybu, pdb_00009fnn, not shown in illustration), a cytosolic protein that works together with BcsQ and BcsR to activate BcsA.

Once it exits the inner membrane and enters the periplasmic space, the cellulose strand is modified to make it even stickier; three copies of an inner membrane protein called BcsG (shown in dark blue) add lipid-derived phosphoethanolamine (pEtN) groups to the growing cellulose chain, forming pEtN-cellulose. Note that the catalytic domain of BcsG was not resolved in the published structure, and is not shown in the illustration. The pEtN-cellulose polymer is released to the exterior of the cell after passing through a channel formed by BcsC (pdb_00009b8h, shown in green), an outer membrane beta barrel protein with numerous TPR motifs that extend into the periplasm.

Another major component of E. coli and Salmonella biofilms are long protein polymers. The dominant protein is called curli: a sticky, hair-like fiber made of numerous stacked copies of the protein CsgA (shown in shades of yellow/orange, pdb_00008c50). Curli are functional amyloids, and share a very similar molecular structure as proteins that form the pathological filamentous plaques of neurodegenerative diseases like Alzheimer's and Parkinson's. In curli, however, these filaments are built deliberately and put to work as structural scaffolding.

Bacterial cells have evolved safeguards to ensure that curli fibers form in a controlled way. A dedicated channel (shown in shades of pink) formed by a nine-fold symmetric ring of CsgG (pdb_00004uv3), forms a 36-stranded β-barrel that is capped by a cage-like vestibule in the periplasm. At its center sits a narrow constriction that is just under a nanometer wide. CsgF (pdb_00006si7 and pdb_00006l7c) is an accessory protein that binds to the CsgG channel and forms a second constriction site which is thought to play an important role in curli secretion and assembly. The narrow pores of the CsgG-CsgF complex ensure that CsgA can only pass through in an unfolded, single-file strand, which keeps it from aggregating until it emerges safely on the cell surface. Rather than relying on ATP or an ion gradient to power transport, secretion is driven by the polymerization of the fiber, which pulls the chain outward. CsgA folds and forms fibers with the help of another protein, CsgB (not shown in illustration), which nucleates filaments and helps keep filaments attached to the cell surface. pEtN-cellulose is also thought to support this process.