Team:Marburg/Killswitch

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Killswitch Database

The field of Synthetic Biology provides a large toolbox of methods and procedures towards the engineering of organisms with unique abilities which we make use of in various ways, for example by taking advantage of their production efficiency in biotechnology or by devoting them as tools for research. However, both approaches have in common that the success stories of these organisms have started in a petri dish in a lab, an area enabling us to work under controlled conditions. Especially, the evolutionary capabilities of bacteria have facilitated those to survive in almost any conceivable surrounding which delegates responsibility to us in terms of biosafety, in order to assure that a possible escape of the generated organisms from the lab does no harm to the outside world.

Therefore, in the past years, several iGEM teams did their best to design a killswitch, a genetically engineered circuit based conditioning of the organism on gene inducing or repressing signals to survive in the lab, but not outside of it. Since science relies on both documentation and analysis of data to make progress, our team decided to summarize the available information of all killswitches designed since 2011 resulting in a killswitch database. Here we show the fast and efficient provision of information considering the killswitch database by using the example of a statistical analysis of the participating iGEM teams in correlation with the number and features of designed killswitches.

A synopsis of the participating teams in total from every continent and those which provided a killswitch reveals that especially the teams in North America, Asia and Europe increased their interest in biosafety (Fig.1 A, B, C). At the same time, the analysis illustrates a higher average number of participating teams from those continents which indicates a more prominent iGEM community there as well. On the other hand, Africa, South America and Oceania have sent a fractional part of teams in relation to the already mentioned continents (Fig.1 F, E, D).

Figure 1: Comparison between the teams participating in the iGEM competition from different continents.

Taking the number of killswitches worldwide into account, normalized to the total number of teams, an increase within the past 4 years becomes obvious. As illustrated in Figure 2, the number of killswitches duplicated during that period of time.

Figure 2: General development of killswitch designing teams from 2011-2014.

A major aspect in the killswitch design is the usage of inducing or repressing signals. The sort of substance which was used ranged from well-established but expensive, synthetic compounds like IPTG and L-Rhamnose to physiologically produced fatty acids or even light. As shown in Figure 3, IPTG was the most favored synthetic inducer/repressor which might be based on the experience many labs have with IPTG-dependent systems. However, the statistical analysis shows no significant preference regarding the choice of repressing/inducing signals. In general, the percentage of both balances each other.

Figure 3: Usage of inducible and repressive compounds in killswitch design.

More important than the choice of inducing or repressing signal is the determination of the target structure which is meant to be affected to kill the cell. Besides interference on RNA or DNA level, membrane-associated systems were chosen to be targeted by the killswitch which might be due to the various accessible weak points, both in membrane synthesis and homeostasis, whereas metabolic aspects and biofilm formation are more complex targets to focus on. Apparently, the majority of the killswitches were designed as a general concept, rather variable than concretely describing target structure or repressive substance.

Figure 4: Target structures chosen by the teams.

The statistical analysis of the described aspects of the last years’ killswitches is an example of how our killswitch database can provide valuable information considering almost every aspect which is important for the design of a custom switch. The overview will allow other teams to scan through the existing designs to pick their parts and improve the systems according to their own needs.
For further informations download our Killswitch-Database:
Killswitch-Database

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