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June 28, 2007

Hacking microbiology

Two science news articles (here and here) about J. Craig Venter's efforts to hack the genome (or perhaps, more broadly, hacking microbiology) reminded me of a few other articles about his goals. The two articles I ran across today concern a rather cool experiment where scientists took the genome of one bacterium species (M. mycoides) and transplanted it into a closely related one (M. capricolum). The actual procedure by which they made the genome transfer seems rather inelegant, but the end result is that the donor genome replaced the recepient genome and was operating well enough that the recepient looked like the donor. (Science article is here.) As a proof of concept, this experiment is a nice demonstration that the cellular machinery of the the recepient species is similar enough to that of the donor that it can run the other's genomic program. But, whether or not this technique can be applied to other species is an open question. For instance, judging by the difficulties that research on cloning has encountered with simply transferring a nucleus of a cell into an unfertilized egg of the same species, it seems reasonable to expect that such whole-genome transfers won't be reprogramming arbitrary cells any time in the foreseeable future.

The other things I've been meaning to blog about are stories I ran across earlier this month, also relating to Dr. Venter's efforts to pioneer research on (and patents for) genomic manipulation. For instance, earlier this month Venter's group filed a patent on an "artificial organism" (patent application is here; coverage is here and here). Although the bacterium (derived from another cousin of the two mentioned above, called M. genitalium) is called an artificial organism (dubbed M. laboratorium), I think that gives Venter's group too much credit. Their artificial organism is really just a hobbled version of its parent species, where they removed many of the original genes that were not, apparently, always necessary for a bacterium's survival. From the way the science journalism reads though, you get the impression that Venter et al. have created a bacterium from scratch. I don't think we have either the technology or the scientific understanding of how life works to be able to do that yet, nor do I expect to see it for a long time. But, the idea of engineering bacteria to exhibit different traits (maybe useful traits, such as being able to metabolize some of the crap modern civilizations produce) is already a reality and I'm sure we'll see more work along these lines.

Finally, Venter gave a TED talk in 2005 about his trip to sample the DNA of the ocean at several spots around the world. This talk is actually more about the science (or more pointedly, about how little we know about the diversity of life, as expressed through genes) and less about his commercial interests. It appears that some of the research results from this trip have already appeared on PLoS Biology.

I think many people love to hate Venter, but you do have to give him credit for having enormous ambition, and for, in part, spurring the genomics revolution currently gripping microbiology. Perhaps like many scientists, I'm suspicious of his commercial interests and find the idea of patenting anything about a living organism to be a little absurd, but I also think we're fast approaching the day when we putting bacteria to work doing things that we currently do via complex (and often dirty) industrial processes will be an everyday thing.

posted June 28, 2007 04:13 PM in Things that go squish | permalink


Although there will probably be large barriers for genome transplantaion for mammalian and eukaryotic cells, it's quite different (and a lot easier) for prokaryotic cells, since there is a lot less epigenetic information to reprogram. Part of the problem with creating oocytes via nuclear transfer is all the regulatory protein gunk that goes with it in the nucleus, from histones to histone binding proteins, DNA methylation, and so on. For the prokaryotes, they were able to simply transform the cells with naked DNA, sans protein, which would be impossible with eukaryotes. So I think the technology will easily generalize to many prokaryotes, but will stall with eukaryotes.

Posted by: such.ire at June 29, 2007 08:09 AM