K.rhaeticus iGEM - chassis for engineered living materials
Synthetic biology holds promises for many new classes of technologies. One such class is physical manufacturing through biology - i.e. growing our everyday products instead of making them.
This might sound far-fetched until you realize that the cell is an approximation of a universal chemical synthesizer. The number of different proteins that can be produced through combination of 20 amino acids in a 1000 amino acid protein is 10^1301 (far greater than the number of atoms in the known universe) and that the anatomy of most animals is more complex than the vast majority of things we use on a daily basis, including cars and phones (possibly minus the chips inside them). Combining these two things with the fact that biology uses cheap and ubiquitous raw materials means that, fundamentally speaking, manufacturing through biology is very much a future possibility. It is already in full swing in chemical manufacturing and in alternative food sources. What we lack today is knowledge - the ability and knowhow to control and guide these organisms to our will, particularly when it comes to producing 3D objects. In other words, the field of synthetic developmental biology is very much in its nascency.
I joined Tom Ellis' lab in my undergrad at Imperial College to learn how to design and control complex genetic circuits. As a result, I became a member of Imperial's 2014 iGEM team, and we narrowed our project down to working on bacterial cellulose - an ultrapure and ultra-strong form of cellulose produced by certain Gluconacetobacter species. This was a fascinating area, because the bacterium could not only be useful for its material production purposes, but theoretically be engineered to control the way it synthesized and shaped the material itself - at least once we learned how to control 3D growth and patterning. In other words, it held the promise to be a platform for synthetic morphogenesis. To do that though, it first needed to be established as a model organism. The genome sequences of the major strains were unknown, and molecular biology tools and methods were not developed. In essence, there was simply no established way to engineer it. That's what I aimed to do during iGEM - establish this bacterium as a model organism within the 4 months we had.
The highest known nanocellulose producing strain at the time was Gluconacetobacter xylinus. However, we had substantial difficulty receiving that strain, so in order to make progress, I isolated a strain from a local vendor of Kombucha pellicle - a natural mixture of yeast and cellulose producing bacteria.
That turned out to be a great decision. First, I was able to quickly find and establish plasmid backbones and transformation methods to engineer it, while the original Gluconacetobacter xylinus resisted engineering much more substantially. As I got up to speed and learned how to do genome sequencing, we decided to sequenced the genomes of both - and it turned out the bacterium I'd isolated was from a different genus/species (K. rhaeticus) and unknown to science - so I named it K. rhaeticus iGEM. While this was ongoing, other members of the team learned how to functionalize nanocellulose with other elements - particularly proteins to bind to heavy metals (with the idea being to produce a thin heavy metal filter). After 4 months of 16-hour days and at great cost to my personal health, that effort got us a bunch of awards and the 2nd prize out of 200+ teams. Continuing to work on this after iGEM, I discovered two other important things. First, Tom and I came up with a way to turn its cellulose production ability on and off at will (otherwise always on by default) - a key ability to make working with it easy. And second, I discovered that this bacterium seemed to need no nitrogen to grow - it could produce cellulose sheets in a medium composed of sugar and vitamins/minerals only. This hinted that it might be nitrogen fixing - but despite combing through its genome, I could not explain how that was possible - it was missing known nitrogen fixation gene clusters. This latter part is a mystery still to be solved.
K.rhaeticus iGEM cells encased in nanocellulose
Interestingly, the original Gluconacetobacter xylinus resisted our attempts to engineer it to the very end - we were able to get the plasmids in and propagate, but rarely any production of recombinant protein. Later, Tom found that this was likely because it contained CRISPR systems - and that we likely would have failed, had I stuck to this species alone. Talk about luck favoring the prepared.
While I decided to move on before we got to doing synthetic morphogenesis on it, engineering this bacterium has become a sub-field of its own. We published our project in two papers across PNAS and Scientific Reports, which spawned multiple grants and over 60 follow-on papers from various labs, including engineering biomaterial composites, light-controlled patterning and production of self-dyeing textiles, as well well as two companies (PurAffinity and Modern Synthesis) - both founded by members of our iGEM team. PurAffinity aimed to functionalize the bacterial cellulose with proteins that captured specific water contaminants to build new kinds of water filters and Modern Synthesis engineered the strain in various ways to produce animal-free leather and coloring.
So the idea of growing our technologies instead of manufacturing them is alive and well. As a field, we still suck at synthetic morphogenesis. But now, there are at least ways to start learning how to do it.