Primary Research: Redesigning Life

 

Creative commons attribution, Photo by Zappys Technology Solutions.
Creative commons attribution, Photo by Zappys Technology Solutions.

Redesigning Life: The Quest for Synthetic Yeast

By Rahul Sharma

Through the Synthetic Yeast 2.0 (Sc2.0) project, researchers are attempting to create a completely synthetic version of the Saccharomyces cerevisiae (baker’s yeast) genome. This will be the first attempt to create a eukaryotic organism (an organism whose cells have a nucleus) with a completely synthetic set of chromosomes. However, researchers are not making a yeast genome identical to that of natural yeast. Such modified yeast might, for example, be designed to withstand low-nutrient environments, or even to produce therapeutic drugs.1

The Sc2.0 project involves over 300 scientists and researchers from five different countries. I assisted with the synthesis and repair of mutations in two chromosomes. Before I and my colleagues in Dr. Karen Zeller’s lab at Johns Hopkins University began begin synthesizing chromosomes, scientists at all involved institutions agreed on what changes to make to the genome. By making these changes, scientists can examine how dramatically a genome can be altered and still remain viable. Researchers can also use these altered chromosomes to study the importance and interactions of various genes.

Once the preliminary design of the synthetic chromosomes is complete, we produce these chromosomes through a bottom-up approach. This approach begins with short, factory-ordered DNA fragments, which are sewn together with the polymerase chain reaction (PCR), a technique that mimics DNA replication. Once the pieces are made big enough, PCR is no longer used. Instead, fragments are inserted into yeast cells, where the yeast’s own intrinsic DNA-repair mechanisms will then stitch the fragments into even longer strands.2 This process is successively repeated in the yeast until all the yeast’s natural genes are replaced with a completely synthetic genome. This bottom-up synthesis is significantly different from current genetic engineering methods. These methods involve the modification or transfer of one or two natural genes, while we are making changes throughout the whole genome.3

One of the biggest goals of the project is to create a minimal genome, one that contains the minimum number of genes required to support life. By identifying a minimal genome, researchers construct a template to which they can add other genes, eventually creating specialized cells for applications in the fields of energy production and health. To obtain this minimal genome, scientists add a specific 35 base-pair DNA sequence to the beginning and end of every non-essential gene in the yeast genome. These 35 base-pair sequences, known as loxp recombination sites, allow for an enzyme called cre-recombinase to bind to these locations. The cre enzyme makes double stranded breaks and pinches off the unwanted genes in between the loxp sites, permanently removing them.2,4

There are many different ways two loxp sites can recombine when the non-essential gene between them is excised. This allows for many variations of the yeast genome that the scientists are now screening.5 They’re looking for the genetic variations that produce the fittest yeast: that is, the kinds of yeast that grow fastest, or the ones that can survive under conditions which would kill natural yeast. Scientists can then sequence the genomes of these yeast varieties to learn what genetic changes caused such characteristics.

The Sc2.0 project highlights the potential of intentional biology, the attempt to redesign life in order to reach a practical end. The future completion of this designer yeast genome will represent an important milestone for synthetic biology. The ability to create fully synthetic genomes allows researchers to exert an extraordinary amount of control over organisms.   Using this technique, researchers can change entire metabolic and developmental pathways within an organism much more rapidly than they could with other gene editing methods. Although the project is still in the early stages, artificial yeast strains could someday be used to create organisms that synthesize vaccines, antibiotics, and even biofuels.1,6 This project will push the field of synthetic biology into a new era, revealing the powerful potential of a man-made, fully-functioning synthetic cell.

References:

1Konig, Harald, Daniel Frank, Reinhard Heil, and Christopher Coenen. “Synthetic Genomics and Synthetic Biology Applications Between Hopes and Concerns.” CG Current Genomics 14.1 (2013): 11-24.

2Annaluru, Narayana, Sivaprakash Ramalingam, and Srinivasan Chandrasegaran. “Rewriting the Blueprint of Life by Synthetic Genomics and Genome Engineering.” Genome Biol Genome Biology 16.1 (2015)

3 Dymond, Jessica, and Jef Boeke. “The Saccharomyces Cerevisiae SCRaMbLE System and Genome Minimization.” Bioengineered 3.3 (2012): 170-73.

4Nagy, Andras. “Cre Recombinase: The Universal Reagent for Genome Tailoring.” Genesis 26.2 (2000): 99-109.

5Dymond, Jessica S., Sarah M. Richardson, Candice E. Coombes, Timothy Babatz, Héloïse Muller, Narayana Annaluru, William J. Blake, Joy W. Schwerzmann, Junbiao Dai, Derek L. Lindstrom, Annabel C. Boeke, Daniel E. Gottschling, Srinivasan Chandrasegaran, Joel S. Bader, and Jef D. Boeke. “Synthetic Chromosome Arms Function in Yeast and Generate Phenotypic Diversity by Design.” Nature 477.7365 (2011): 471-76.

6Andrianantoandro, Ernesto, Subhayu Basu, David K. Karig, and Ron Weiss. “Synthetic Biology: New Engineering Rules for an Emerging Discipline.” Mol Syst Biol Molecular Systems Biology 2.1 (2006)