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A DEVELOPMENT OF SYNTHETIC BIOLOGY
Kodikos Labs: a company meant to understand synthetic biology chassis
Antoine Danchin
Agnieszka Sekowska
Many industrial biological applications are difficult to reconcile with the evolution of natural organisms. The absence of goal of life makes it somewhat incompatible with the existence of the human goals that are specific to industrial designs. This discrepancy is at the core of the work developed at Kodikos Labs. Kodikos Labs owns a unique model of cell behaviour in stationary phase. This model is used in particular for the study of ageing, and the actions that can be implemented to delay it.
Identifying what leads organisms to evolve is seen as directly associated with the generation of viable offspring. This is why the exponential growth state is the preferred laboratory state for studying cells, especially microorganisms. In this context, long-term evolutionary studies favour either growth in chemostats (Marliere et al., 2011) or the daily repetition of diluting cells in fresh medium (Good et al., 2017), allowing them to grow again. However, the life of cells is mostly spent in the absence of growth. The aim of creating Kodikos Labs' proprietary cell model is to explore what happens to the progeny of cells when they are left to survive in a medium where they can no longer grow. Once understood, this model is used to systematically explore the consequences of altering their environment. This makes it possible to discover unexpected consequences of the presence of molecules present in normal metabolism, but also of any synthetic compound.
In order to understand whether this survival allows the cells to
discover, genetically or epigenetically, solutions to remedy their
lack of growth, Kodikos Labs has developed a
well-characterised bacterial model - the complete genome sequence of
the initial state of the bacteria in question has been determined - of
« intelligent » Escherichia coli, capable of evolving in
such a way as to inform us of their modes of interaction with their
environment. This model allows both the genetics of the processes
being studied to be modified (by modifying the genome of the bacteria
in an appropriate way) and the environment (by modifying the culture
medium).
These cells can, on a solid medium, grow sufficiently to form small
colonies, but stop growing due to the depletion of the sources of
carbon usable by their metabolism (known thanks to the metabolic
reconstruction allowed by our up-to-date annotations of their genome).
The main experiment that allowed us to develop this model consisted of
adding to the medium various carbon sources that these cells cannot
use because of regulatory blockages, but which can in principle be
used by these cells if they have been able to modify, genetically or
epigenetically, the regulatory locks (Sekowska et al., 2016).
A first experiment showed that this model is very effective in revealing a behaviour that was initially unexpected, but that the results of the experiments made it possible to understand, namely the appearance of adaptive mutations over time. In short, the cells deposited on Petri dishes form small colonies within 24 hours, which remain as such for a few days. Then, generally from the fourth or fifth day - and this for a period of two months - small papillae form on some of these colonies. In the course of time, these papillae increase in size until they practically invade the whole box. Phenotypic analysis shows that these new cells are able to use the available carbon source that their parents could not. The sequencing of the genome of a hundred of these mutant bacteria has allowed us to discover the appearance of concerted sets of mutations, and above all to understand their cause (Sekowska et al., 2016). It should be remembered here that the initial strain is by no means mutant, and that the mutations observed are not at all randomly distributed either in the chromosome or in functional terms. The cause of these mutations is now understood: transcription, which opens the DNA double helix, is mutagenic, both because it increases the deamination of cytosines by at least a hundredfold, but also because it makes guanine derivatives vulnerable to the action of reactive oxygen species (ROS, oxidative stress). It is therefore the genes expressed preferentially in stationary phase that are subject to this specific mutagenesis process. This explains why mutations are not distributed randomly. It is also this knowledge that allows the strain to be manipulated in such a way as to try to answer the questions posed by Kodikos Labs' clients.
It is important to understand here that the observations obtained from the proper study of this model cannot be protected by patent (infringement would be impossible to prove), but instead correspond to a unique know-how, protected in the annotations of a specific database of the totality of the genes of the proprietary model, and strictly confidential. An important point is that this data evolves in real time, modified according to experiments, and that its value only increases with time (provided that the company is in business).
The chassis as the forgotten partner of Synthetic Biology
What would we need if we were to construct from scratch a long-lived organism? This question is essential for scaling up Synthetic Biology (SynBio) processes. It requires us to try and make a thorough inventory of functions, taking care not to forget unobtrusive but essential ones. To this aim, we separate cells into two independent components, the cell (the chassis) and its program. A general trend of SynBio has been to focus on the functions necessary for reproduction (i.e. growth). At some point, later on, we will need to see what happens when cells simply survive, and connect survival to longevity and death.
The most difficult part of SynBio is the understanding of the connection between information and its material embodiment as a « chassis ». This is reflected in the two origins of biology: chemistry (as biochemistry) and genetics. It is usually difficult to make people understand what genetics is, and how it can be used as a scientific proof rather than biochemistry.
Here is a summary of the first workshop of an US-EU task force, focusing on synthetic genomes.
Putting molecular biology and computer sciences in perspective, we rprpose to develop the practice of SynBio with recursivity and information at its core. The processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations.
Inevitable metabolic accidents
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The aging chassis
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Antifragility
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