The GencoCon 2010 Award

GenoCon was started in 2010 by RIKEN BASE. Each GenoCon Contest iteration focuses on a specific synthetic biology problem, and provides participants with a virtual laboratory (built on semantic web technology) for designing genetic solutions to the challenge problem. The GenoCon 2010 challenge problem was to develop a system for eliminating airborne formaldehyde in a model plant system, by using 2,000 base-pairs of synthetic DNA or less.

Of the 66 submissions, 6 contestant designs (along with several controls and researcher designed sequences) were constructed and tested for growth in the presence of different concentrations of formaldehyde and at different growth stages by the RIKEN Plant Science Center.

To evaluate the sequence designs, we first synthesized DNA fragments and transformed them into Arabidopsis (follow this link for details). Then we measured for formaldehyde tolerance – the ability of the transformant Arabidopsis to grow of under various formaldehyde concentrations in their media.

Since formaldehyde causes plant damage, transformant plants that can detoxify formaldehyde must show stronger growth than the wild type plants that were used as controls. After the experiments, almost all transformant plants showed better growth than the wild type control plants, so we confirmed that most of the designs passed this challenge of our assignment.

GenoCon scored the success of each design from the experimental results, and the GenoCon comittee made a comprehensive review and awarded winners in multiple categories.

GenoCon Award trophies hold actual transgenic Arabidopsis thaliana plants designed by the award winners. The plants are dried before preservation.

GenoCon 2010 Award Winners

Based on the experimental results, we selected Masahiro Mochizuki for the Best Design Award. In evaluation, the GenoCon committee gave the highest rating to Masahiro Mochizuki’s idea for showing the best results in increasing the number of stoma in the evaluation experiments, and for the innovative quality of his original idea report.

We selected High School student Makoto Sugisaki for the Excellent Design Award with a high rating. A freshman at the time of application, Makoto has a deep knowledge on molecular biology and his design showed higher growth ratio performance than even those in the other category for researchers. We would like to continue GenoCon to recruit hidden students with talent like him.

Masahiro Mochizuki also got the Best Idea Award with his interesting idea to add stomagen, which increases stomatal density, even in the very limited DNA length. Since this idea does not directly affect plant tolerance, we could not evaluate his idea effectively. For a true evaluation it is better to check the absorption ratio of formaldehyde. In this case his design showed the best result under 0.75mM conditions. This concentration is strong enough for practical usage.

We selected High School student Makoto Tanaka for the Excellent Design Award. Based on the common sense of our basic knowledge as researchers, we expected his idea of transporting protein to the endoplasmic reticulum (ER transport signal) would not work well. But ER transport showed better growth than using mitochondria transport even in our additional experiment where Researcher B used mitochondria transport signal and Researcher C used ER transport signal.

Unfortunately, Makoto Tanaka used anaerobic archaea enzymes which do not fit with the metabolic pathway of an aerobic plant like Arabidopsis. For this reason his experimental results did not show a better growth ratio. However, Makoto Tanaka’s idea made our researchers realize the new potential of ER transport. This is a successful example of the effective collection and sharing of genome-design theories and programs that let the public participate in research.

We selected Ryo Eto for the Excellent Programming Award, who optimized the codon with a probabilistic stochastic algorithm. His programming code was clear with easy-to-follow instructions. We expect other participants to modify and improve on his code for the next time. We confirmed experimentally that his codon optimization algorithm actually works to create fully functional DNA sequences

Other GenoCon 2010 Results

The design of Researcher A, Professor Izui, showed the highest growth ratio. He used HPS-PHI enzyme fusion, optimized its codon, and added chloroplast transport signal. But only Researcher A used different vector designed to have much higher activity of transcription and translation than that provided to the participants (pMDC32), so the result may be attributed to this high expression vector.

Using an approach different from any of the rest of participants, only RIKEN Researcher D focused on the dihydroxyacetone pathway, attempting formaldehyde detoxification using genes from a fungus. As the result, it showed strong growth ratio under the higher formaldehyde concentration (1.5mM). Normally, it is very difficult to collect DNA fragments of genes from non-model organisms. Since this competition uses chemically synthesized DNA sequence technology, GenoCon encourages free ranging thinking.

GenoCon 2010 Conclusion Summary

As an overall trend of the GenoCon 2010 assay, we confirmed inhibition of plant growth for the submitted transformants under high formaldehyde concentrations. Formaldehyde caused strong stress on leaves and turned them into gray and dark brown. Red anthocyanin also accumulated at the base of leaf stems. Though we considered these damaged areas along with growth ratio in our scoring method, the final result was almost the same even using these two analyses.