Difference between revisions of "Part:BBa K4990002"

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mFadA B-domain

Usage in short

You can use it for specific targeting of Fusobacterium nucleatum(Fn) or achieve bacteria-bacteria adhesion.

What you need to know!

Many bacteria have long chain fiber-protein complexes on their surfaces, which are called pili or fimbriae. These pili are composed of individual pilus monomers that link together end-to-end in the extracellular environment, self-assembling into long chain fibers with high physical strength.

For Fusobacterium nucleatum, its pili are referred to as Fusobacterium adhesin A (FadA). The monomers that make up these pili come in two forms: ①pre-FadA, which serves as an anchoring structure, attaching the entire pilus to the bacterial inner membrane. ②mature FadA (mFadA), which can link head-to-tail and self-assemble into a long filament.

Our project aims to accomplish bacteria-bacteria targeting. To accomplish this, we intend to utilize the self-assembly property of mFadA. We have used the surface display technology to fuse a bacterial pilus monomer onto a membrane protein of the engineered bacterium, which we call the "fishing rod protein" . The membrane protein acts as the fishing rod, the linker serves as the fishing line, and the bacterial pilus monomer functions as the bait. By displaying the fishing rod protein, our engineered bacteria can essentially "fish" for target bacteria, enabling precise bacteria-bacteria targeting.

However, displaying the entire bacterial pilus monomer directly on the surface would lead to a range of issues, including steric hindrance, nonspecificity, and metabolic waste. Therefore, we truncated the mFadA to address these concerns.

What it is?

Below is the structure of the mFadA B-domain, which is truncated from the pili monomer of Fn:

It functions like bait, enticing the Fusobacterium nucleatum to take the hook.

What can it do?

However, not the entire structure of mFadA is involved in self-assembly. Thus, we considered removing unnecessary domains. Upon closer examination of mFadA's structure, we divided it into two domains: Domain A and Domain B. Domain A comprises two anti-parallel α-helical structures, while Domain B consists of a single anti-parallel α-helix. We believe that Domain B is the most crucial. On a microscale, it possesses the function of binding with Domain A, and on a macroscale, it exhibits the capability to target Fn (Fusobacterium nucleatum).

Therefore, by displaying the engineered bacteria with the mFadA B-domain on their surface, specific adhesion to Fn can be achieved, enabling bacteria-to-bacteria targeting to become reality.

How does it work?

The following are detailed microscale contacts involved in the self-assembly of mFadA.

Notice

1.The residue numbering is based on the complete mFadA sequence, rather than renumbering after truncation of domain A or B.

2.The protein sequence of mFadA can be referred to in this article: Han YW, Ikegami A, Rajanna C, et al. Identification and characterization of a novel adhesin unique to oral fusobacteria. J Bacteriol. 2005;187(15):5330-5340. doi:10.1128/JB.187.15.5330-5340.2005

3.The information regarding contacts related to self-assembly mentioned above comes from this article: Nithianantham S, Xu M, Yamada M, Ikegami A, Shoham M, Han YW. Crystal structure of FadA adhesin from Fusobacterium nucleatum reveals a novel oligomerization motif, the leucine chain. J Biol Chem. 2009;284(6):3865-3872. doi:10.1074/jbc.M805503200

Two mFadA monomers were sourced from reference [1]. The mFadA protein sequence from Fn ATCC10953 was selected, and structural prediction was conducted using Colabfold. Employing the Rosetta local_docking method, a total of 100,000 rounds of Monte Carlo-based repeated docking were performed, leading to the successful identification of the optimal self-assembly outcome. The obtained assembly closely resembles the binding mode described in reference [2], as illustrated in the diagram below：

We further identified the microscale contacts between the two mFadA monomers. These contacts are categorized into primary and secondary hydrophobic interactions, as well as salt bridge interactions, as depicted in the diagram below

It is worth noting that while the hydrophobic structure formed by leucine chains makes a significant contribution to the self-assembly, the salt bridge shell formed by four pairs of acidic and basic residues envelops these hydrophobic centers, providing stability to the binding.

It can do more!

Novo targeting method

Diverging from conventional methods, we have innovatively harnessed the self-assembly of bacterial pili for targeting. These protein fibers, formed by monomers connecting end-to-end, are present on the surface of bacteria. However, their variations differ significantly among various bacterial species. Hence, we can capitalize on this shared feature and diversity to craft a tailored, engineered approach for specific bacterial targeting.

Apart from the FadA we've been using (PDB ID: 3ETW), there are many similar pili structures, such as S. pyogenes pili (PDB ID: 3B2M), Pseudomonas aeruginosa pili - CupE (PDB ID: 8CIO), uropathogenic E. coli - Type I pili (PDB ID: 6Y7S), and E. coli biofilm protein CsgA (PDB ID: ). If we could utilize the self-assembly of these similar pili, it would enable specific targeting of these bacteria.

Novo display method

Here are 4 problems with common bacterial surface display systems: 1.Passenger protein size is limited; 2.Ukaryotic proteins are difficult to fold correctly in prokaryotic systems; 3. Passenger proteins exert survival pressure on host cells; 4. Limitations of Antibiotic Resistance in Engineering Applications.

However, our novel surface display system can circumvent all of the aforementioned issues. By adding a truncated pilus tag to the passenger proteins, they can be produced by other bacteria, and the chassis bacteria only need to display a single anchor on the surface to achieve the surface display of high-molecular-weight proteins. Similarly, if passenger proteins are produced by eukaryotic cells, it is possible to achieve the surface presentation of eukaryotic proteins on prokaryotic cells. Furthermore, the impact of surface display on the growth of chasis cells is minimized. In addition to this, due to the adhesive properties of the pili, this feature can be utilized for selection instead of relying on antibiotic resistance. Therefore, the two-step surface display method achieved by pili self-assembly can address many traditional issues. However, the application of this method is limited by the strength of binding between pili monomers. Nevertheless, we believe that this can be addressed through protein engineering and directed evolution methods.

Although these limitations exist, with the extensive development of microbial genomics and proteomics research, along with a deeper understanding of the genetic background, cell surface structure, and function of environmentally advantageous microbial communities, researchers will continue to develop bacterial surface display systems that cater to various needs.

Reference

[1]Han YW, Ikegami A, Rajanna C, et al. Identification and characterization of a novel adhesin unique to oral fusobacteria. J Bacteriol. 2005;187(15):5330-5340. doi:10.1128/JB.187.15.5330-5340.2005

[2]Nithianantham S, Xu M, Yamada M, Ikegami A, Shoham M, Han YW. Crystal structure of FadA adhesin from Fusobacterium nucleatum reveals a novel oligomerization motif, the leucine chain. J Biol Chem. 2009;284(6):3865-3872. doi:10.1074/jbc.M805503200

[3]Témoin S, Wu KL, Wu V, Shoham M, Han YW. Signal peptide of FadA adhesin from Fusobacterium nucleatum plays a novel structural role by modulating the filament's length and width. FEBS Lett. 2012;586(1):1-6. doi:10.1016/j.febslet.2011.10.047

Sequence and Features