Friday, September 16, 2011

Is There Anything Synthetic Biology Can't Do?

Synthetic biology involves the creation of new forms of life that have never existed before. These new lifeforms will be designed to produce valuable products such as fuels, medicines, high value chemicals, food products for animals and humans, and more.
Biologists have built two artificial chromosome arms and put them to work in a living yeast. They plan to replace the entire yeast genome over the next five years and then evolve new strains to order.

"Nothing like this has ever been done before," says Jef Boeke of the Johns Hopkins University School of Medicine in Baltimore, Maryland, who is leading the research. As well as designing and building the new genome from scratch, his team has come up with a way to systematically scramble it to produce new strains.

The artificial yeast are similar to Craig Venter's synthetic cells, announced last year. Venter replaced the entire genome of a bacterium with a synthetic genome – but the task is far harder in yeast, because it is a more complex organism and has a bigger genome. _NewScientist
Science is very early into the project of synthetic biological organisms, but no matter how slowly the progress, the information learned will be invaluable.
Yeast has 16 chromosomes, all of which have been sequenced. Boeke started small, replacing the right arm of chromosome 9 and part of the left arm of chromosome 6. He began by designing the new sequences on a computer, using the known sequence as his starting point. He stripped from this virtual DNA all the meaningless "junk" DNA, which does not code for proteins. Then he added markers called loxPsym at the ends of all non-essential genes – those that could be changed or deleted without killing the yeast. In the real world, these markers can be attacked by an enzyme called Cre, which swaps genes between the marker sites. Finally, he created these new sequences in the lab using the chemical building blocks of DNA, and inserted them into a living yeast in place of its natural chromosome arms.
Shuffling genes

"This is another remarkable example of how synthetic biology can be used to rewrite chromosome sequences at a sizeable scale," says Daniel Gibson of the J. Craig Venter Institute in Rockville, Maryland. He says it could help us understand the rules governing genome structure.

For instance, the reshuffling technique can test how different arrangements of genes affect the yeast. Boeke has already done this by shuffling the genes on the artificial chromosomes using the Cre enzyme.

"You can take a yeast gene and insert it somewhere else in the genome, and you tend to get a healthy yeast," Boeke says. That suggests a reshuffle wouldn't matter, but different yeasts consistently use the same order. "Maybe there are hidden rules of genome structure that we can distil," Boeke says.
Make your own yeast

Boeke now intends to repeat this re-engineering process with the other chromosomes in yeast. Once the entire genome is laced with loxPsym sites, Boeke plans to use Cre to make wholesale changes. Because the method targets only non-essential genes, and does not interfere with their internal structure, it should mostly produce healthy yeast. _NS
Very ambitious indeed. And it is just the beginning.

Proterro is a biotech company that aims to produce high volumes of low-cost sugars from water, CO2, sunlight, and basic nutrients -- using their own custom designed micro-organism.
Proterro’s patent-pending biosynthetic process combines an engineered photosynthetic microorganism with an advanced high-density, modular solid-phase bioreactor to provide a fermentation-ready feedstock, called Protose. Produced by combining only water, carbon dioxide, sunlight and nutrients in the biosynthetic process, Protose is projected to cost less than such feedstocks as sugar cane and cellulosics, and can be used to produce a variety of commercial scale fuels and chemicals through standard industrial fermentation methods. _BiofuelsDigest_via_BrianWestenhaus
Proterro's plan is ingenious, but time is a critical factor. If the company cannot produce high volumes of its sugar reliably and economically within the next 5 years, it will probably be crowded out of the market by the other companies highlighted in the article linked above.

Biomass can be grown over 80% of the Earth's surface -- land or ocean -- and does not require the care that special microbial bioreactors require. Dozens of companies are devising better ways to produce cheap sugars from biomass, and at least a few of them are likely to come up with profitable approaches within the next 5 years. Once cheap biomass sugars are available, the cost of making biofuels and other renewable chemicals will suddenly become less of an obstacle.



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