Friday, January 25, 2008

It's ALIVE...well, not quite yet

Folks over at the J. Craig Venter Institute have reported today in the journal Science that they have successfully synthesized an entire bacterium genome. An entire 580,000+ base-pair genome. From scratch. This is quite momentous as it brings the Venter team this much closer to their goal of synthesizing life de novo.

In case you have been living in a cave for the past 10 years, Craig Venter is one of the scientists that successfully sequenced the human genome back in 1999. For the past several years, he and his team of researchers at the JCVI have been working on creating artificial life - or rather synthetically recreating actual life. The first step towards this goal was accomplished just this past summer when Venter et al. successfully inserted the genome of one bacterium into another bacterium, essentially turning one species into another. Basically they showed that it was possible to insert whole genomes into another cell. The latest step just accomplished was to actually synthesize a whole genome. Next will be to try to get this genome inserted into a cell - which seems likely to happen considering their success in step 1. In fact, I would expect such an announcement in the near future.

This latest effort is quite interesting - they first sequenced the genome of Mycoplasma genitalium and then built "small" segments of the DNA (~5,000 - 7,000 bp long) from individual nucleic acids (Phase 1). To ensure that they could identify their genome, the researchers inserted their own "watermark" sequences that differentiated it from the natural M. genitalium genome. They also took some precautions by disabling genes for infectivity. They then assembled these "cassettes" into larger pieces of ~24,000 bp. These 24k pieces were then cloned into E. coli for replication so there was enough DNA to work with for the next phase. Phases 2 and 3 was similar to phase 1 - this time joining the 24k fragments into 72k pieces, which were again cloned into E. coli for amplification and sequencing, and then joining 72k fragments together to form 144k pieces, again cloned and amplified in E. coli. Phase 4 involved joining 144k fragments to create 288k fragments. However, at this point the researchers could not obtain E. coli clones with the 288k half-genome and had to move the operation over to the yeast Saccharomyces cerevisiae. Once that was done, Phase 5 was a simple matter (HAH!) of joining the half-genome chunks together through homologous recombination in yeast cells. Final sequencing showed that the team had indeed synthesized the entire M. genitalium.

What's next? Well, step three again will be to insert this synthesized DNA into a host cells to derive fully functioning M. genitalium. After that? How about creating an entirely novel genome from scratch? Then how about synthesizing self-assembling cell membranes to house these novel genomes? The rate at which the JCVI team is suceeding, I don't think we'll have to wait very long for true synthetic life.

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