Craig Venter and the unknown 50 genes of life

Last Friday, I attended an event in Berkeley which was part of the Bay Area Science Festival, Craig Venter spoke as part of a promotional tour for his new book “Life at the Speed of Light” and it was a fascinating talk, another blog post will follow with a write up to the talk and his response to my question to him about Biotech Moonshots. As some of you know, I’ve become convinced that Venter is one of the few scientists in our industry focused going for Biotech moon shoots akin to Elon Musk (which has proven to be a very controversial opinion in the hacker groups and Citizen science communities that I’m a part of).

During part of his talk, Venter mentioned an interesting realization they made during the construction of the first synthetic organism, it turned out that there were 50 genes that they had to include in the first synthetic organism that had unknown function. Without these 50 genes the new cell wouldn’t “boot up” and live and it made me wonder, what are those critical genes and what do they do that’s so critical to life?

It’s first important to clarify where Venter and his team started on the design of the synthetic genome which was (from the journal Science):

“Design of the M. mycoides JCVI-syn1.0 genome was based on the highly accurate finished genome sequences of two laboratory strains of M. mycoides subspecies capri GM12 ”

The further I started to dig into this genome the more time I realized it would take, it wasn’t simply the case of finding the genes with unknown function but digging through the data to find it. Here’s the graphic attached to the Science paper which provides a visual overview of the synthetic genome:

http://bamh1.com/wp-content/uploads/2013/10/Gibson.SOM_.pdf

After a while I was able to find the genebank entry for the entire synthetic organism, just identifying those genes which have unknown function seems like it might need some custom scripts, anyone interested in running a quick script and sending me a list of the 50 Unknown function genes? If so, the story will continue!

http://www.ncbi.nlm.nih.gov/nuccore/296455217?report=genbank&to=1078809