Scientists create functional 'designer chromosome'

An international team of scientists said Thursday they have synthesized the first working chromosome for yeast in what they called a "major advance" for " designer" microorganisms that could produce novel medicines, raw materials for food, and biofuels. Over the past five years, scientists have built bacterial chromosomes and viral DNA, but this is the first report of an entire eukaryotic chromosome, the threadlike structure that carries genes in the nucleus of all plant and animal cells, built from scratch, the team reported. "It is the most extensively altered chromosome ever built. But the milestone that really counts is integrating it into a living yeast cell," said Jef Boeke of the Langone Medical Center at New York University, who led the study. "We have shown that yeast cells carrying this synthetic chromosome are remarkably normal. They behave almost identically to wild yeast cells, only they now possess new capabilities and can do things that wild yeast cannot," Boeke said. In the U.S. journal Science, the team reported how, using computer-aided design, they built a fully functioning chromosome, which they call synIII, and successfully incorporated it into brewer's yeast, known scientifically as Saccharomyces cerevisiae. Yeast chromosome III was selected for synthesis because it is among the smallest of the 16 yeast chromosomes and controls how yeast cells mate and undergo genetic change, the team said. The effort to construct synIII, which took seven year, tied together some 273, 871 base pairs of DNA, shorter than its native yeast counterpart, which has 316,667 base pairs. Boeke and his team made more than 500 alterations to its genetic base, removing repeating sections of some 47,841 DNA base pairs, deemed unnecessary to chromosome reproduction and growth. Also removed was what is popularly termed junk DNA, including base pairs known not to encode for any particular proteins, and " jumping gene" segments known to randomly move around and introduce mutations. Other sets of base pairs were added or altered to enable researchers to tag DNA as synthetic or native, and to delete or move genes on synIII. "When you change the genome you're gambling. One wrong change can kill the cell," said Boeke. "We have made over 50,000 changes to the DNA code in the chromosome and our yeast still live. That is remarkable. It shows that our synthetic chromosome is hardy, and it endows the yeast with new properties." The team was able to manipulate large sections of yeast DNA without compromising chromosomal viability and function using a so- called scrambling technique that allowed the scientists to shuffle genes like a deck of cards, where each gene is a card. "We can pull together any group of cards, shuffle the order and make millions and millions of different decks, all in one small tube of yeast," Boeke said. "Now that we can shuffle the genomic deck, it will allow us to ask, can we make a deck of cards with a better hand for making yeast survive under any of a multitude of conditions, such as tolerating higher alcohol levels." Using the scrambling technique, the researchers said they will be able to more quickly develop synthetic strains of yeast that could be used in the manufacture of rare medicines, such as artemisinin for malaria, or in the production of certain vaccines, including the vaccine for hepatitis B, which is derived from yeast. Synthetic yeast, they said, could also be used to bolster development of more efficient biofuels, such as alcohol, butanol, and biodiesel. "Our research moves the needle in synthetic biology from theory to reality," Boeke said, adding that the team's next steps involve synthesizing larger yeast chromosomes, faster and cheaper.