Project Biolink

3D printing of bacterial biofilms, linked together through nanowires

Project Description

In this section we describe the Problem and Solution, our Biolink project as well as an overview of the synthetic biology and printing process in the project.

Problem and Solution

Biofilms are communities of bacteria connected by protein nanowires and surrounded by an extracellular matrix. In this form, they are more resistant and can severely affect human health, industrial productivity and the environment. More precisely, biofilms can cause infections in the human body, affect water quality, and damage industrial installations and equipment. Research and industry have been working to find various solutions for preventing and removing this threat. Potential solutions, such as health products, drugs and industrial removal products, are tested on artificially formed biofilms.

Generic placeholder image — Figure 1. Fields and industries affected by detrimental biofilms (4Inno.com)

The problem with biofilms formed artificially is that they are time consuming, difficult to control and to reproduce. This means that artificial biofilms do not reflect natural biofilm characteristics, making product testing unreliable. Therefore, biofilm-removal products may have a different effect when used in natural settings, with unforeseen negative side-effects and reduced efficiency.

Our project is entitled Biolink and provides an alternative to current biofilm formation technologies. We use a 3D printer, which we call The Biolinker, to form layers of a designed bioink made of bacteria that can bind together into a desired structure.

Biolink helps biofilm-related industries in several ways. First, it brings reproducibility and control to how bacterial biofilms can be artificially formed. Second, biofilm printing adds automation and scalability, making biofilm formation processes more efficient, and thus, cheaper. Hence, Biolink can help to design safer and more effective anti-biofilm solutions by increasing biofilm testing process efficiency and resemblance to reality.

The Biolink Project

Our printing system, called Biolink, can be summarized in the following sentence: biofilm producing bacteria are printed with the help of a flexible scaffold hydrogel. First of all, our homemade bacteria (modified to make biofilms) are mixed with a solution of sodium alginate and subsequently with calcium chloride. There, the Ca2+ molecules keep the structure fixed creating a stable gel. This hydrogel-bacteria mixture is then induced with rhamnose, a sugar specific for our promoter, which makes them synthesize CsgA, the linking molecule. CsgA proteins polymerize to an amyloid structure surrounding the cells and connecting them to each other through the scaffold. Once the cells are all attached in the structure defined by the gel scaffold, it is no longer necessary. Consequently, the hydrogel is dissolved with sodium citrate. But the cells are still connected due to the curli amyloid! So, we obtain a perfectly defined 3D structure made of bacteria.

(SLIDESHOW HERE)

The Biolink project promotes the open source and educational spirit of iGEM. Our 3D printer, the Biolinker, is made of K’NEX construction toys, a DIY solution that is both easy to build and efficient in doing its job. Through policy and practice we try to position our project within the synthetic biology industry and academia, as well as observe socio-economic perception and feedback. We accomplish this by analyzing and interviewing stakeholders, treating ethical and regulatory issues, and building a business plan around our project.

Synthetic Biology in our Project

During biofilm formation, bacteria produce an extracellular matrix made of amyloid structures. These amyloid structures are curli fimbriae, composed of intertwined filaments with a thickness of approximately 4-7 nm (Nguyen, 2014). Therefore, curli production helps bacteria bind to each other in natural biofilms (Taylor et. al. 2012). There are two distinctive operons involved in this highly regulated pathway; csgBA and csgDEFG. The csgBA operon encodes for two proteins: CsgA and CsgB. The csgDEFG operon encodes for the proteins required for the transport of CsgA and CsgB to the cell surface (Dueholm et al, 2011).

On one hand, CsgA is an amyloid protein that acts as monomer for curli formation. On the other hand, the protein CsgB in an integral membrane protein, which binds CsgA to the cell; CsgB acts as an anchor for curli formation. CsgA is transported as an unfolded protein to the extracellular matrix. Once outside the cell, it aggregates with CsgB and the self-assembly of these aggregates form the amyloid fibrils. When CsgA comes in contact with CsgB, the fibrils bind to another cell and the process is repeated again until an entire network has been created (Barnhart et al, 2006).

In our project, we designed an inducible system for synthesizing CsgA in biofilm-making deficient cells. Besides to that, we aimed to create a customized biofilm. To do so, we designed different biobricks that contain a peptide tail attached to the sequence of the biofilm protein CsgA that provides a specific surface affinity. In the end, we planned to use our engineered cells (which also express a fluorescent reporter) for printing in different layers; printing biofilms in 3 dimensions.

The Bioink and Alginate as Supporting Scaffold

In initial experiments printing with bacterial cells dispersed in LB media it quickly became obvious, that a supporting scaffold would be required: due to surface interactions the liquid spread out creating a final thickness of the printed line of almost one centimeter. In tissue engineering sodium alginate is commonly used as a synthetic extracellular matrix material (Rowley et al., 1999). Inspired by this, we took a look at sodium alginate to use as a scaffold material. Sodium alginate is a carbohydrate polymer which can be fairly well dissolved in water, but in contact with calcium ions (or other divalent cations) the polymers are connected via electrostatic interactions forming a hydrogel. Made for instance from LB, this hydrogel could provide bacterial cells with everything they need for weeks and keep them alive. Furthermore, jellification is a reversible process by complexing the calcium ions with citrate and replacing it again with sodium ions (Rowley et al., 1999). Thus, we had found a substance ideally meeting our purpose of being initially liquid, capable of rapidly turning into a viscous gel and reversing this process again.

Strains

The strains used for our project are described here

Escherichia coli K-12 MG1655 PRO ΔcsgA ompR234

This strain of Escherichia coli, used in previous studies of amyloid fiber production in bacteria, is characteristic for having knocked-out the CsgA gene. However, it has all the other genes required for formation of the curli structure.

We have used this strain for our project as the main organism for the printing process. As the bacteria cannot express csgA, we transformed our strains with a plasmid containing this gene under the control of an inducible promoter. Consequently, we can modulate where and when the amyloid fiber will be formed! (Chen, A.Y., et al. 2014)

Escherichia coli Top10

This strain was used exclusively for highly efficient transformations. We used this organism for cloning experiments, plasmid isolations and other basic steps of our project.