Yet more intramolecular cross-links in Gram-positive surface proteins

Intramolecular covalent bonds in Gram-positive bacterial surface proteins

Gram-positive bacteria experience considerable mechanical perturbation when adhering to host surfaces during colonization and infection. They have evolved various adhesion proteins that are mechanically robust to ensure strong surface adhesion. Recently, it was discovered that these adhesion proteins contain rare, extra intramolecular covalent bonds that stabilize protein structures and participate in surface bonding. These intramolecular covalent bonds include isopeptides, thioesters, and ester bonds, which often form spontaneously without the need for additional enzymes. With the development of single-molecule force spectroscopy techniques, the detailed mechanical roles of these intramolecular covalent bonds have been revealed. In this review, we summarize the recent advances in this area of research, focusing on the link between the mechanical stability and function of these covalent bonds in Gram-positive bacterial surface proteins. We also highlight the potential impact of these discoveries on the development of novel antibiotics and chemical biology tools.

An ester bond underlies the mechanical strength of a pathogen surface protein

Gram-positive bacteria can resist large mechanical perturbations during their invasion and colonization by secreting various surface proteins with intramolecular isopeptide or ester bonds. Compared to isopeptide bonds, ester bonds are prone to hydrolysis. It remains elusive whether ester bonds can completely block mechanical extension similarly to isopeptide bonds, or whether ester bonds dissipate mechanical energy by bond rupture. Here, we show that an ester-bond containing stalk domain of Cpe0147 is inextensible even at forces > 2 nN. The ester bond locks the structure to a partially unfolded conformation, in which the ester bond remains largely water inaccessible. This allows the ester bond to withstand considerable mechanical forces and in turn prevent complete protein unfolding. However, the protecting effect might be reduced at non-physiological basic pHs or low calcium concentrations due to destabilizing the protein structures. Inspired by this design principle, we engineer a disulfide mutant resistant to mechanical unfolding under reducing conditions.

Bacterial surface adhesion proteins are characterized by unusual mechanical properties. Here, the authors use atomic force microscopy-based technique to study a surface-anchoring protein Cpe0147 from Clostridium perfringens and show that an ester bond can withstand considerable mechanical forces and prevent complete protein unfolding.

Probing the potential of CnaB-type domains for the design of tag/catcher systems

Building proteins into larger, post-translational assemblies in a defined and stable way is still a challenging task. A promising approach relies on so-called tag/catcher systems that are fused to the proteins of interest and allow a durable linkage via covalent intermolecular bonds. Tags and catchers are generated by splitting protein domains that contain intramolecular isopeptide or ester bonds that form autocatalytically under physiological conditions. There are already numerous biotechnological and medical applications that demonstrate the usefulness of covalent linkages mediated by these systems. Additional covalent tag/catcher systems would allow creating more complex and ultra-stable protein architectures and networks. Two of the presently available tag/catcher systems were derived from closely related CnaB-domains of Streptococcus pyogenes and Streptococcus dysgalactiae proteins. However, it is unclear whether domain splitting is generally tolerated within the CnaB-family or only by a small subset of these domains. To address this point, we have selected a set of four CnaB domains of low sequence similarity and characterized the resulting tag/catcher systems by computational and experimental methods. Experimental testing for intermolecular isopeptide bond formation demonstrated two of the four systems to be functional. For these two systems length and sequence variations of the peptide tags were investigated revealing only a relatively small effect on the efficiency of the reaction. Our study suggests that splitting into tag and catcher moieties is tolerated by a significant portion of the naturally occurring CnaB-domains, thus providing a large reservoir for the design of novel tag/catcher systems.

An internal thioester in a pathogen surface protein mediates covalent host binding

To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a ‘chemical harpoon’. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions.

DOI:http://dx.doi.org/10.7554/eLife.06638.001

The human body is home to many trillions of microbes; most are harmless, but some may cause disease. To live inside a host, microbes must first attach to host tissues. This process involves multiple proteins on each microbe's surface, called adhesins, which interact with the molecules that make up these tissues.

Like all proteins, adhesins are long chains of simpler building blocks called amino acids, and each amino acid is connected to the next via a strong ‘covalent’ bond. Adhesins, however, typically attach bacteria to host molecules through the combined strength of many weak ‘non-covalent’ interactions.

It was recently discovered that one adhesin from a bacterium called Streptococcus pyogenes contains a rare, extra covalent bond—called a thioester—in an unusual location between two of its amino acids. S. pyogenes is a common cause of throat infections in humans, and can also cause the life-threatening ‘flesh-eating disease’.

Walden, Edwards et al. have now used a range of computational, biochemical, structural biology and cell-based techniques to study other adhesins that have thioester bonds in more detail. Computational searches identified hundreds of bacterial proteins containing similar bonds. These included many from bacteria that infect humans: such as Streptococcus pneumoniae, which is the most common cause of pneumonia in adults; and Clostridium difficile, which is notorious for causing severe gut infections in hospital patients. Closer examination of the three-dimensional structures of three of these proteins—including one called SfbI from S. pyogenes—revealed that each had a clear thioester bond. Biochemical tests of an additional nine of the identified proteins strongly suggested they too contained thioester bonds.

Walden, Edwards et al. then showed that SfbI was able to not only attach to tissues like conventional adhesins, but also chemically react with fibrinogen: a human protein that is essential for blood clotting and commonly found in inflamed tissues and healing wounds. This chemical reaction results in the formation of a covalent bond between SfbI and fibrinogen, which is as stable as the bonds that link the amino acids in a protein chain. Further experiments revealed that SfbI strongly binds to human cells grown in the lab under conditions that mimic tissue inflammation. Finally, Walden, Edwards et al. made a mutant version of SfbI that did not contain a thioester, and found that it could not interact with fibrinogen nor bind to human cells.

Together, these findings suggest that thioesters in bacterial adhesins act like ‘chemical harpoons’, which microbes can use to irreversibly attach themselves to molecules within their host's tissues. This attachment mechanism has not been seen before in host-microbe interactions, and further research is now needed to explore whether interfering with this process could represent a new way to treat bacterial infections.

DOI:http://dx.doi.org/10.7554/eLife.06638.002