Hopkins undergraduates build novel genome

It is certainly more difficult to make foods from scratch than to purchase their ready-to-eat counterparts. Creating pancake batter and then grilling them to the perfect golden-brown requires a lot more effort than popping a couple of frozen pancakes in the toaster. Squeezing fresh oranges to make orange juice takes more energy than pouring a glass of orange juice from concentrate.

By that same logic, creating an entire organism’s genome from scratch via piecing together and reworking fragments of DNA required an immense amount of effort: seven years’ worth, to be exact.

With the help of Hopkins undergraduate students in the “Build-A-Genome” class, scientists have created the world’s first synthetic yeast chromosome from scratch. Led by Jef Boeke, a former professor of molecular biology and genetics at the Hopkins and now the director of the Institute for Systems Genetics at New York University, a global team of researchers began this collaborative endeavor in 2007. After seven years of hard work, their study was published last Friday in the journal Science.

Since 2007, approximately 60 Hopkins students have participated in Build-A-Genome, an upper-level synthetic biology class offered by the biomedical engineering department in the Whiting School of Engineering. These students, who come from both the Krieger School of Arts & Sciences and the Whiting School of Engineering, include Murat Bilgel, Pavlo Bohutski, Kristin M. Boulier, Brian J. Capaldo, Joy Chang, Kristie Charoen, Woo Jin Choi, Peter Deng, James E. DiCarlo, Judy Doong, Jessilyn Dunn, Jason I. Feinberg, Christopher Fernandez, Charlotte E. Floria, David Gladowski, Pasha Hadidi, Isabel Ishizuka, Javaneh Jabbari, Calvin Y. L. Lau, Pablo A. Lee, Sean Li, Denise Lin, Matthias E. Linder, Jonathan Ling, Jaime Liu, Jonathan Liu, Mariya London, Henry Ma, Jessica Mao, Jessica E. McDade, Alexandra McMillan, Aaron M. Moore, Won Chan Oh, Yu Ouyang, Ruchi Patel, Marina Paul, Laura C. Paulsen, Judy Qiu, Alex Rhee, Matthew G. Rubash kin, Ina Y. Soh, Nathaniel E. Sotuyo, Venkatesh Srinivas, Allison Suarez, Andy Wong, Remus Wong, Wei Rose Xie, Yijie Xu, and Allen T. Yu. Many of these genome creators have already graduated.

Synthetic biology is an emerging area of study that applies the principles of engineering to living systems. The project completed by Boeke’s team marks a major turning point in the field of synthetic biology: although synthetic chromosomes have been reported, Boeke’s study is the first ever to report a synthetic eukaryotic chromosome. Eukaryotes, a taxonomical classification that includes plants and animals, describe organisms with cells that contain a nuclei. Prior to Boeke’s study, other research teams had only synthesized bacterial and viral DNA.

The creation of an artificial yeast chromosome involved many steps. Boeke and his team used computer software to design synIII, a modified version of yeast chromosome III. SynIII was then incorporated into Saccharomyces cerevisiae, commonly known as brewer’s yeast. Yeast chromosome III was chosen out of yeast’s 16 chromosomes because of its relatively small size and its influence over both yeast mating behaviors and the incorporation of genetic changes.

The researchers spent seven years stitching together the synthetic chromosome from pieces of DNA. The synIII chromosome contains 272,871 base pairs, slightly fewer than the 316,617 base pairs in native, or natural, yeast chromosome III. Hopkins undergraduate students in the Build-A-Genome class performed much the work, spending their class and homework time stringing together bits of DNA into longer segments.

Boeke’s research team manipulated these bits of DNA ina way that persuaded the chromosome to generate new, desirable features. The team performed more than 500 tweaks to the native yeast genome, removing repeated sections and so-called junk DNA. Additionally, the researchers added tags to the DNA to label it as native or synthetic.

The yeast containing synthetic DNA behaved almost identically to wildtype yeast. Furthermore, the researchers were able to shuffle the yeast genes like a deck of cards by using a genetics technique called scrambling. With this technique, the researchers could generate millions upon millions of different decks of genetic cards. This mixing created completely novel genetic sequences.

Eventually, if the field of synthetic biology continues to expand, researchers may be able to assemble synthetic strains of yeast for the production of medicine, vaccines, biofuels, and even beer. With synthetically grown building blocks, medications and vaccines, such as artemisinisn, a malaria drug, and the hepatitis B vaccine, could become more accessible. Synthetically grown yeast may also improve the efficiency of biofuel and beer production.

Boeke’s study has inspired scientists around the world to synthesize the 15 other chromosomes found in yeast from scratch. Work is already underway in laboratories in the United Kingdom, China, India, and the United States.

Although the preparation processes require more time and effort, most people can agree that made-from-scratch pancakes and hand-squeezed orange juice taste better than frozen pancakes and orange juice from concentrate. Likewise, although synthesizing yeast from scratch requires a lot of time and effort on the part of scientists and researchers, the results will most likely be more rewarding than if they had simply ordered yeast specimens from a scientific catalogue.