Addressable and adaptable intercellular communication via DNA messaging

Abstract

Engineered consortia are a major research focus for synthetic biologists because they can implement sophisticated behaviors inaccessible to single-strain systems. However, this functional capacity is constrained by their constituent strains’ ability to engage in complex communication. DNA messaging, by enabling information-rich channel-decoupled communication, is a promising candidate architecture for implementing complex communication. But its major advantage, its messages’ dynamic mutability, is still unexplored. We develop a framework for addressable and adaptable DNA messaging that leverages all three of these advantages and implement it using plasmid conjugation in E. coli. Our system can bias the transfer of messages to targeted receiver strains by 100- to 1000-fold, and their recipient lists can be dynamically updated in situ to control the flow of information through the population. This work lays the foundation for future developments that further utilize the unique advantages of DNA messaging to engineer previously-inaccessible levels of complexity into biological systems.

Tuning Interdomain Conjugation Towardin situPopulation Modification in Yeast

“…Perhaps more interesting for future work, however, would be to target more complex functions in recipient cells, such as modifying metabolic pathways in a consortia producing a useful product, or disrupting quorum sensing function in virulent cells, for example, by targeting the farnesol pathway in C. glabrata . Recent work has furthermore demonstrated the capacity of conjugative DNA transfer to tune intercellular messages in a synthetic E. coli consortium 22 , and such a strategy could very feasibly be expanded to a wide range of both DNA programs and recipient species. This gets to the heart of IDC’s power: unlike other perturbation strategies such as Type VI Secretion Systems, which have been used for targeted killing 75,76 , the possibilities for recipient-programming via IDC are only as limited as our ability to engineer the DNA for those functions and express them in recipient populations, as well as the frequency of conjugative delivery.…”

“…In addition to focusing primarily on eliminating specific populations, few of these tools are targeting for modifying fungal microbiome members. In contrast, bacterial conjugation, a naturally occurring form of horizontal gene transfer (HGT) 17 allows modification of bacterial populations instead of simple killing and has already been used for probiotics 18 , defense against antibiotic-resistant pathogens 19 , crop modification for desired traits 20 , control of undomesticated microbial species 21 , circuit-like control of synthetic consortia 22 , and in situ microbiome engineering 23,24 . Bacteria also conjugate with a variety of eukaryotic recipient cells, most commonly from bacterial donor Agrobacterium tumefaciens to plant cells 25 .…”

Applications of Serine Integrases in Synthetic Biology over the Past Decade

“…This process inspires researchers to rearrange the orientation of attP/attB sites to utilize them for other synthetic biology and bioengineering applications. For example, when attP/attB sites are located in two different linearized DNA, the two strands will exchange partial fragments specifically to create two recombined DNA strands (Figure 2b) [31]. This strategy can also be developed as multiple linear DNA assembly in one pot [32].…”

Identifying LasR Quorum Sensors with Improved Signal Specificity by Mapping the Sequence–Function Landscape

“…The use of engineered bacterial consortia to distribute tasks among different strains has gained great interest in various applications, such as biomanufacturing, , bioremediation, , therapeutics, , and agriculture. , This strategy can offer reduced cellular burden of microbial members and the ability for specialization that leverages each microorganism’s traits. − For engineered bacterial consortia to function robustly, programmable cell–cell communication is required to coordinate processes in different cells and control their spatiotemporal dynamics, which has been achieved via diffusible chemical intercellular signaling, − cell–cell adhesion, , and conjugal transfer of DNA. − In nature, bacteria commonly communicate via diffusible quorum sensing signals to elicit population-level and cell density-dependent responses. − Various quorum sensing signals have been used as chemical signals in engineered microbial consortia, including oligopeptides, , γ-butyrolactone, and homoserine lactones. − Among these, homoserine lactones (HSLs) have been most widely utilized in synthetic biology due to the relative ease of signal production and sensing. − In these systems, the canonical LuxR-type allosteric transcription factor binds to its cognate HSL ligand, and after complexation, activates transcription from its corresponding quorum sensing promoter. , HSLs for LuxR-type regulators contain a lactone ring and commonly an acyl chain that can vary in length (4 to 20 carbons), degree of saturation, and oxidation state at the third carbon. , Structural similarity can cause noncognate HSL signals to activate LuxR-type quorum sensors resulting in signal crosstalk, − which can be problematic for precise control of functions in microbial consortia when using multiple quorum sensing systems.…”