Beaker Hill: Synthetic Biology @ iGEM 2008 (Part 3)

H.pylori is prevalent worldwide, infecting about half the world’s population, and is primarily responsible for the formation of ulcers. It is also designated a type I carcinogen by the WHO. This species of bacteria is able to readily infect people because of a small mutation in one of its proteins, flagellin, which prevents it from being recognized by our immune system. The team from Slovenia produced a modified version of the H.pylori flagellin protein which enabled the “toll-like receptor” proteins of the immune system to react to it. However, the trick is that the change was slight enough that when “regular” H.pylori was introduced to the mice they used for their tests, the immune system also responded!

It’s a real case of threading the needle: changing the protein enough so the immune system picks it up, but not so much that the naturally-occuring form of the bacteria was unrecognizable. To add to their accomplishments, the team actually used their modified flagellin in two ways: by producing and purifying the protein itself to use as a vaccine, and by preparing the DNA so that human cells which present foreign proteins can produce flagellin and activate the immune system that way.

Finally, no discussion of synthetic biology, and iGEM in particular, would be complete without an overview of one of the driving concepts behind the competition. Somewhere in the sprawling expanse of MIT you can find the lab behind the Registry of Standard Biological Parts. As mentioned in Part 1 of this series, the idea behind the Registry is extremely sound: one day, it is hoped, future synthetic biologists will be able to choose from a gigantic list of DNA sequences—“parts” with defined functions—from the Registry, combine them and pop them into their bacteria to create a new function. The DNA parts (which are actually stored at MIT and shipped to iGEM teams or others who want to use them) are called BioBricks, and one of the missions of iGEM is to expand the roster of BioBricks for subsequent years.

While this approach works marvelously on paper, there have been persistent flaws in its execution which existed back in 2006 and have yet to be rectified. One nearly universal complaint from the teams we talked to is that not all of the BioBricks actually do what they are supposed to, meaning the teams had to make their own versions of parts that they could get “off the shelf”. To achieve the future goal of being able to pick from a defined list of parts and set them up in a system, reliability of the parts in question is absolutely vital.

The second major drawback stems from the way in which BioBricks become “standard parts.” (A quick sidebar: restriction enzymes are proteins which cut strands of DNA in the middle of a very specific short sequence unique to each particular enzyme. The sequence each enzyme recognizes is called a restriction site.) BioBricks are “standard” in that each one contains the same restriction sites at each end of the DNA sequence encoding the part itself. The part, obviously, cannot contain any of the restriction sites; otherwise, adding the enzyme to the system would cut in the middle and ruin the area you need. This means that to put any two parts together, you can cut them using the same restriction enzymes, and then the loose ends fit together perfectly.

So instead of hunting for places to cut and join two pieces of DNA, when using BioBricks you know exactly where to cut, and that the cuts you make won’t destroy the part. However, a funny thing often happens: given that the restriction sites are very short sets of DNA, and there are only four letters used to build a DNA sequence, having one in the middle of your part is not particularly uncommon. (Given the way that DNA is responsible for coding proteins, there is a way to change your sequence and keep the results the same.) A couple of the teams related stories of having created a working part only to ruin it by trying to convert it into BioBrick form. Somehow we doubt this was the goal of this system.

Given that the cost of simply putting together a DNA sequence from scratch has been dropping steadily over the last several years, it seems more likely that this may be the future direction for synthetic biology. Will the BioBrick/Registry format have a place in this future? Most of the teams foresaw a combination of BioBricks and on-the-fly DNA synthesis going forward. But regardless of how we continue the work of synthetic biology, the projects we saw showed the promise and relevance of this work for the future.