Life with Four Billion atoms

Thursday, April 23, 2009 - 6:00pm
Tom Knight MIT CSAIL and Ginkgo Bioworks, Inc.
Tom Knight

Today it is commonplace to design and construct single electronic components with billions of transistors. These are complex systems, difficult (but possible) to design, test, and fabricate. Remarkably, simple living systems can be assembled from a similar number of atoms, most of them in water molecules. Key ideas of intentional simplification, effective design tools, and stratified designs will help us understand, engineer, and build these simple organisms.

In this talk I will present the current status of our attempts at full understanding and complexity reduction of one of the simplest living systems, the free-living bacterial species Mesoplasma florum. Our recent experiments using transposon gene knockouts identified 354 of 683 annotated genes as inessential in laboratory culture when inactivated individually. While a functional redesigned genome will certainly not remove all of those genes, this suggests that roughly half the genome can be removed in an intentional redesign.

I will discuss our recent knockout results and methodology, and our future plans for:

  • Genome re-engineering using targeted knock-in/knock-out double recombination
  • Re-sequencing of additional strains of Mesop