Basic Parts

In my first post, I provided a very brief description of what synthetic biologists call parts. We use these parts to build more complicated systems. But this seems too obvious. Doesn't every construction job require parts? As I noted before, we know from everyday experience that standardized parts in general make jobs more efficient. The construction crew starting with trees and lumps of metal would get the job done eventually, but their approach is incredibly inefficient. To my knowledge, the only system of standard biological parts in widespread use is that which was invented by Tom Knight at MIT. These parts are called BioBricks.

A BioBrick is a DNA part that carries out a defined function and adheres to prescribed standards. BioBrick parts are divided into two categories: basic parts and composite parts. This post focuses on basic parts, but I will be devoting a post to composite parts very soon. Basic parts have one particular, narrow function. They are like screws and 2x4s—it is only when they are put together to make composite parts that they do something useful. Examples of basic parts include promoters, which can be thought of as switches that turn other parts on and off, protein coding sequences, and transcriptional terminators, which mark the end of a collection of protein coding sequences that are read together.

The most important standard for BioBricks is that they all have the same pattern of restriction sites, which are sequences of DNA bases that are recognized by a cognate enzyme. The enzyme chops the DNA in two across the double helix at the restriction site. BioBricks utilize restriction enzymes that cut the DNA in a Z shape so that overhangs are left behind. These overhangs are called sticky ends, and if two pieces of DNA share complementary sticky ends they can be spliced together. The usefulness of this tool cannot be overemphasized. As a matter of fact, the discovery of restriction enzymes was the subject of the Nobel Prize in Physiology or Medicine in 1978. One of the recipients was Hamilton Smith, who was among the scientific leadership of the M. mycoides JCVI-syn1.0 project last year.

BioBricks are designed to all have the same pattern of restriction sites: a prefix containing an EcoRI site followed by XbaI site upstream of the functional DNA of the BioBrick, and then a suffix containing a SpeI site and a PstI site on the tail end. The names of these restriction sites aren't terribly important, but they are derived from the names of the bacteria where they are natively found. Tom Knight chose these particular restriction sites for a very good reason. Of all of the combinations of these four restriction sites, only two—XbaI and SpeI—generate complementary sticky ends. Since these sites are immediately adjacent to the BioBrick part, it allows two distinct parts to be assembled one after the other, leaving the standard BioBrick prefix and suffix around the new composite part. This process is described visually and in greater detail here.

The significance of BioBricks is that since the same assembly procedure is used every time, laboratory practices are more streamlined and the parts one lab generates can be shared with every lab in the world that uses the BioBrick method. The Registry of Standard Biological Parts aims to do just that. A huge variety of parts are maintained by the Registry, which is based at MIT. The list of parts is set up like a shopping catalog, grouped into categories by function. Each part is assigned a unique number, which makes labeling culture and microfuge tubes in the lab a breeze! For example, the promoter from the famous lac operon is given the nice round number R0010, where the R stands for "regulatory."

Labs that are affiliated with the Registry receive a distribution of parts every year in the form of dried DNA. In 2010, each team received 1152 distinct parts in 3 microtiter plates that together took up less space than my lab notebook. This means that even small institutions like mine can accumulate a massive repertoire of parts without needing overly expensive equipment. And parts not included in the main distributions can be requested from the Registry and mailed.

This fact has very powerful implications. The biological equivalent of a massive warehouse can be stored in the compact form of DNA, shipped across the world, and mixed and matched in endless combinations.

In my next post I will be talking about GFP and other basic parts used to make bacteria change color. In the meantime, please feel free to post comments, follow me on Twitter (@ericmsawyer), and subscribe to the RSS feed.

Image Credit: Shetty, R (via Registry of Standard Biological Parts)

References and Further Reading:

Endy, D. Foundations for Engineering Biology. Nature 438, 449–453 (2005).

J. Craig Venter Institute. First Self-Replicating Synthetic Bacterial Cell.

Registry of Standard Biological Parts.