Current tools and technologies for on-demand production of organisms are limited by the number and scope of transformation capabilities, continuous and rapid production capability, and the lack of secure public repositories for academics and industry containing the necessary organismal design and characterization information. Today, we have a number of host microbes for which we have a satisfactory, though not extensive, understanding of their metabolism and sufficient genetic tools that we can use for reliable engineering. Engineering of plant and animal cells is expanding, especially given particular applications (e.g., CAR-T cell engineering), but still faces significant bottlenecks.
Breakthrough Capabilities & Milestones
Ability to grow any host, anytime, in a controlled and regulated setting.
Establish protocols for the development of media that support cellular viability for non-model organisms.
Robust screening of useful hosts beyond model organisms.
Develop robust, high-throughput screens for rapidly assaying useful properties in libraries of organisms.
Use output of high-throughput screens/sensors and computer control to amplify a signal or expand a cell line that produces a product of interest.
Routine domestication of non-model organisms through DNA delivery and genetic modification.
For related reading, please see Gene Editing, Synthesis, and Assembly.
Catalog and assay current methodologies and tools for carrying out DNA delivery in microbial/mammalian systems (e.g., viral vectors, conjugations, biochemical methods) and plant systems (e.g., Agrobacterium-, biolistic-, nanomaterial-based methods).
Develop high-throughput methods that can be done in parallel for DNA delivery (using standard methods) into non-model hosts.
Establish a suite of gene-editing tools for the rapid insertion and/or deletion of genetic elements in diverse primary mammalian cells.
Characterize basic DNA parts for expression strength in non-model organisms, specifically a larger library of plants.
Development of well-characterized and robust insertion sites in plant genomes.
Develop high-throughput, genome-wide editing tools for non-model organisms.
Establish robust temporal and/or spatial control of gene expression in mammalian cells.
Develop broad-host-range vectors for a variety of model and non-model organisms.
Develop high-throughput, targeted editing and rapid genome-evolution tools that couple genetic changes to phenotypic changes.
Develop universal approaches to transforming any plant.
Routine genetic manipulation of any non-model host in less than one week from first isolation.
Ability to build and control small molecule biosynthesis inside cells by design or through evolution.
Identify model organisms for performing specific types of chemistries or organisms that have native precursor biosynthesis pathways for specific classes of molecules.
Precise temporal control of gene expression for well-studied systems.
Construct a limited number of model host organisms for synthesizing all-natural products.
Construction of single-cell organisms for production of unnatural derivatives of natural products.
Temporal control over multiplexed regulation of many genes in parallel.
Software and hardware for optimizing titer, rate, and yield of any product produced by any host.
On-demand construction of single cell organisms for production of nearly any molecule of interest, including organic chemicals and polymers.
Spatial control over, or organization of, metabolic pathways in cells and construction of unnatural organelles.
Tools to target heterologous proteins to various subcellular compartments.
Inducible synthesis of organelles.
Gain-control for selective permeability in and out of the organelle.
Methods and tools to reprogram transport of metabolites and compartmentalization of biochemical reactions.
Alter chemical conditions within the organelle/microcompartment.
Multiple orthogonal organelles/microcompartments in the same cell for compartmentalizing different parts of a pathway.
Production and secretion of any protein with the desired glycosylation or other post-translational modifications.7National Research Council (US) Committee on Assessing the Importance and Impact of Glycomics and Glycosciences. (2012). Transforming glycoscience: A roadmap for the future. Washington (DC): National Academies Press (US). View publication.
One or more microbial hosts capable of producing laboratory-scale quantities of a single glycoform of a desired protein.
A few microbial hosts capable of secreting functional versions of proteins with no post-translational modifications.
Ubiquitous control of post-translational modification (including glycosylation of multiple sites with multiple sugars) in a diverse array of hosts.
- Clark, D. S., & Blanch, H. W. (1997). Biochemical Engineering (Chemical Industries) (2nd ed., p. 716). New York, New York: Crc Press.
- Venayak, N., von Kamp, A., Klamt, S., & Mahadevan, R. (2018). MoVE identifies metabolic valves to switch between phenotypic states. Nature Communications, 9(1), 5332. View publication.
- Weinhandl, K., Winkler, M., Glieder, A., & Camattari, A. (2014). Carbon source dependent promoters in yeasts. Microbial Cell Factories, 13, 5. View publication.; Hsiao, V., Cheng, A., & Murray, R. M. (2016). Design and application of stationary phase combinatorial promoters (SEED 2016 Technical Report). Retrieved from MurrayWiki.
- DeLoache, W. C., Russ, Z. N., & Dueber, J. E. (2016). Towards repurposing the yeast peroxisome for compartmentalizing heterologous metabolic pathways. Nature Communications, 7, 11152. View publication.
- Jakobson, C. M., Chen, Y., Slininger, M. F., Valdivia, E., Kim, E. Y., & Tullman-Ercek, D. (2016). Tuning the catalytic activity of subcellular nanoreactors. Journal of Molecular Biology, 428(15), 2989–2996. View publication.
- Kim, E. Y., & Tullman-Ercek, D. (2014). A rapid flow cytometry assay for the relative quantification of protein encapsulation into bacterial microcompartments. Biotechnology Journal, 9(3), 348–354. View publication.
- National Research Council (US) Committee on Assessing the Importance and Impact of Glycomics and Glycosciences. (2012). Transforming glycoscience: A roadmap for the future. Washington (DC): National Academies Press (US). View publication.
- Sethuraman, N., & Stadheim, T. A. (2006). Challenges in therapeutic glycoprotein production. Current Opinion in Biotechnology, 17(4), 341–346. View publication.