Overview
The main theme of our project is communication. With that in the mind, we chose to work with naturally occurring communication systems. Bacteria are a well established model in synthetic biology, so what a better way of unifying the two and study their communication system? With the field of synthetic biology being relatively new, we believe it is essential in this phase to lay the foundational groundwork for the development of new modular tools.
How do bacteria communicate?
Quorum sensing is a communication system which occurs in natural microbial communities that enables individual bacteria to communicate with each other through chemical signaling. The signaling is given by a molecule, a Homoserine Lactone (HSL), that binds with a sensing receptor, followed by a series of events that will result in a change of expression on key genes. Considering that the molecules produced by each cell can pass through the cell membrane, and so be diffused along the medium, the response will be proportional to the number of cells in the population.
This allows bacteria to sense population density and modulate their gene expression accordingly, resulting in synchronized gene expression and behavior. This type of signaling can also be used, when brought over to synbio and biotechnology, as an inter-cell communication system, with spatial separation. In a solid medium with separated strains or in a bioreactor where only a section of the cells are induced to send the signal, quorum sensing can be used to make a position-based control of gene expression.
There are many different types of quorum sensing systems that are naturally occurring, coming from a wide range of bacterial species, and this diversity can be explored for various applications in the engineering of biological systems. However, only a few of these have been characterized and optimized enough for use in synthetic biology, although not successfully integrated in complex genetic circuits that have been proposed since the initial characterization of these systems, because of difficulties that will be discussed further on. These systems that were shown to work in E.coli were of a particular kind of quorum sensing, called AI-1, in which the signal molecules naturally has the capacity of passing through the cell wall (differing from the AI-2 system, which requires some extra proteins to transport the signaling molecules, and therefore is harder to use with E.coli).
For our project, we chose to work with six quorum-sensing systems: Lux, from Aliivibrio fischerii, Las and Rhl, from Pseudomonas aeruginosa, Cin, from Rhizobium leguminosarum, Tra, from Agrobacterium tumefaciens, and finally Rpa, from Rhodopseudomonas palustris, each one with different synthase and receptor proteins, and different promoter sequence, along with responding natively to correspondant HSL molecules.
How can we improve quorum sensing systems for synthetic biology?
The first step to transpose these elements to the field of synthetic biology is to lay the foundation that will enable us to use these tools. For quorum sensing, one factor that has hindered the development of application these mechanisms in bigger and more complex networks is the lack of orthogonality in quorum sensing systems.
For two signals to be used at the same time, there are two kinds of non-cognate signaling that can occur, chemical and genetic, relating to where systems can interfere in one another. Chemical crosstalk is interference between HSL molecules and receptor proteins, while genetic crosstalk is interference between receptors and promoters.
Recent research has focused mostly on counteracting chemical crosstalk, as it is the more proeminent kind and it is the one that limits the idea of co-cultures, as genetic crosstalk could be dealt with by separating different receptor-promoter pairs in different cells, creating the possibility of using strains with different capabilities in the same bio-process.
Going against this trend, and to add upon it, our project targets genetic crosstalk. Considering the possibility of using only one strain in a bioprocess, but still having the capacity of space-based division of tasks, a circuit having multiple quorum-sensing receptor proteins and promoters in the same cell is needed. Thus, the necessity of expanding our control over genetic crosstalk in these pathways.
This means characterizing how these elements function and their possible interactions, and the implications of those interactions for biological engineering. With all of those things in mind, the main objective of our project was to characterize activity and quantify the genetic crosstalk between a variety of quorum sensing systems that showed promising activity in prior works, while also using this information to predict, model and ultimately aid possible design applications and solutions for microbial communication.
References
- Grant, Paul K et al. “Orthogonal Intercellular Signaling for Programmed Spatial Behavior.” Molecular Systems Biology 12.1 (2016): 849. PMC. Web. 16 Oct. 2018.
- Nathan I Johns, Tomasz Blazejewski, Antonio LC Gomes, Harris H Wang, “Principles for designing synthetic microbial communities”, Current Opinion in Microbiology, Volume 31(2016), Pages 146-153, ISSN 1369-5274, https://doi.org/10.1016/j.mib.2016.03.010.
- Spencer R. Scott and Jeff Hasty. “Quorum Sensing Communication Modules for Microbial Consortia” ACS Synthetic Biology 5.9 (2016), 969-977 doi: 10.1021/acssynbio.5b00286
- N.Kylilis, Z.A. Tuza, G. Stan, K.M. Polizzi. “Tools for engineering coordinated system behaviour in synthetic microbial consortia” Nature Communications, volume 9 (2018), Article number: 2677.
- D.R.Michele, M.R.Yue, H.K.Ann. “Can the Natural Diversity of Quorum-Sensing Advance Synthetic Biology?” Frontiers in Bioengineering and Biotechnology, volume 3 (2015), 2296-4185, doi: 10.3389/fbioe.2015.00030
- R.J.Case, M.Labbate, S.Kjelleberg. “AHL-driven quorum-sensing circuits: their frequency and function among the Proteobacteria” The ISME Journal, volume 2, pages 345–349 (2008)
- M.E.Taga, B.L.Bassler. “Chemical communication among bacteria” Proceedings of the National Academy of Sciences, Nov 2003, 100 (suppl 2) 14549-14554; doi:10.1073/pnas.1934514100