Engineering Biology & Materials Science
Synthesis considers the primary production or creation of material components via engineered biology.
We consider Synthesis as the primary production or creation of material components. In this roadmap, the focus is on the generation of material components via engineered biology. This includes utilizing or exploiting engineered biology to produce monomers, polymers, biomolecules, and macromolecules that serve as components of a material (bulk or otherwise). Key challenges in Synthesis include high-yield production of protein-based natural materials, such as spider silk and elastin, from engineered biology; alternative biological production systems and utilization of natural and non-natural nucleic and amino acids; and enabling re-synthesis or recycling of materials to enable greater sustainability.
Engineering biology has the capability to transform the materials generated through biosynthesis and the catalysts which facilitate their formation. In this depiction, novel monomers with orthogonal reactivity enable sequence-defined polymerization and the precise control of monomer order provides programmed higher order structure. Equally important, this synthesis is carried out by robustly engineered enzymes able to recognize non-natural monomers.
Biological synthesis and/or polymerization of non-natural and/or abiotic chemical monomers, excluding amino acids., ,
Identify and engineer enzymes to recognize and polymerize conventional chemical monomers (e.g., acrylamide).
Develop metabolic pathways to yield chiral cyclic monomers amenable to ring-opening polymerization.
Demonstrate side chain modification of polymeric scaffolds by biological reactions catalyzed by living cells.
Enable vinyl monomer production by engineering metabolic pathways for in situ polymerization reactions.
Expand the library of chemical monomers polymerizable by evolved enzymes.
Engineer complex orthogonal translation systems, including engineered orthogonal ribosomes, for site-directed incorporation of novel (non-amino acid) chemistries into polymers.
Enable complex polymer production (e.g., co-polymers, sequence-controlled polymers, brushed polymers) with enzymatic systems.
Hybrid chemical and biological synthesis methods.,
Characterize and improve the enzymology of orthogonal translation systems (OTSs) for site-directed incorporation of novel chemistries into polymers.
Enable hybrid flow chemistry-biocatalytic synthesis systems.
Full integration of heterogeneous chemical and biological catalysis in modular platforms that are stable after long-term storage and facilitate product switching.
Enable retrobiosynthesis of materials with desired properties, such as thermal conductivity or elasticity.
Engineering Biology (2019) Breakthrough Capabilities
Included in the roadmap are select breakthrough capabilities from our 2019 roadmap, Engineering Biology (below in green; milestones at 2021, 2024, 2029, and 2039). While these breakthrough capabilities were written in the context of advancing the field of engineering biology, the EBRC Materials Roadmapping Working Group leading this roadmapping project felt that the technical achievements elaborated in these breakthrough capabilities and their milestones directly contribute to achieving advancements in materials from engineering biology. This content has been incorporated as reference and, when pertinent, will be provided with context for its inclusion in this roadmap.
PCR, reverse transcription, cellular replication, and transcription of fully unnatural nucleotide-containing genes of up to 400 base pairs.
At this length, unnatural aptamer and aptazyme polymers could be regularly evolved and engineered.
Identification of “missing” functionality or functionalities in A-T-G-C base pairs.
Improved in vitro manipulation of unnatural nucleic acids.
Expansion of unnatural nucleotide toolkit.
Biosynthesis of unnatural nucleotides.
Organisms capable of full replication, maintenance, and transcription of a plasmid or artificial chromosome made up entirely of unnatural bases.
Expanded genetic code systems for translation of >100-amino acid proteins containing fully-unnatural amino acids, and proteins with at least four, distinct unnatural amino acid building blocks.
Implementing unnatural amino acids for materials synthesis will require advancements in translation system engineering, to enable a broader production range from ribosomes. Furthermore, biosynthesis of sequence-defined synthetic biopolymers in which new chemistries (synthetic amino acids or synthetic monomers made-up of non-natural backbones) can be encoded in a template-directed manner, is likely to require the engineering or repurposing of organisms with multiple open coding channels (recoded genomes).
Create proteins that are capable of gaining new, therapeutically-useful activities through unnatural amino acids.
Efficient biosynthesis of proteins containing three or more distinct unnatural amino acid building blocks.
Biosynthesis of unnatural amino acids.
Templated biosynthesis and evolution of new polymers with large user-selected sets of unnatural building blocks in vivo.
Ability to rationally engineer sensor suites, genetic circuits, metabolic pathways, signaling cascades, and cell differentiation pathways.
The engineering of circuits and pathways will be necessary for the synthesis of material components from engineered biology. The engineering of sensor suites and signalling cascades will also be important for the dynamic behaviors of materials, particularly living materials and composite materials that incorporate cells. More on engineering dynamic activities of materials can be found in Properties & Performance.
Reliable engineering of genetic circuits with more than ten regulators for sophisticated computations.
Reliable engineering of novel, many-enzyme pathways utilizing combinations of bioprospected enzymes with well-characterized kinetics.
Five-time improvement and expansion of inducers/promoters for model organisms that respond to environmental inputs and any intracellular metabolite.
Utilize machine-learning approaches to use the vast amount of uncurated literature results within pathway design.
Creation of optogenetic tools for in vivo RNA post-transcriptional control to allow for easy control of any gene expression process through mRNA.
Reliable expression of redesigned synthases to produce secondary metabolites, including polyketides and non-ribosomal peptides.
Computational design of protein-ligand and RNA-ligand interfaces suitable for engineering protein-based or RNA-based sensors.
Simultaneous, tunable, timed expression of many transcription factors controlling mammalian cell state.
Ability to build and control small molecule biosynthesis inside cells by design or through evolution.
In the context of synthesizing materials from engineering biology, design and evolution of cells to build and control the synthesis of monomers, in addition to small molecules, will be important.
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.
Ability to manufacture any targeted glycosylated protein or metabolite using cell-free biosynthesis.
Contributors to this roadmap have indicated that the 2024 milestone “Production of bacterial glycoconjugate vaccines in cell-free systems” would gain significant relevance and value by including the production of bacterial glycoconjugate therapeutic antibodies in cell-free systems, in addition to vaccines.
Ability to build modular, versatile cell-free platforms for glycosylation pathway assembly.
Expanded set of glycosylation enzyme-variants that efficiently install eukaryotic glycans
Production of bacterial glycoconjugate vaccines in cell-free systems.
Expanded set of enzymes capable of glycosylating metabolites in vitro.
Cell-free pipelines to produce and assess the functionality of diverse, human glycosylated protein therapeutics.
Ability to produce any glycosylated protein therapeutics and vaccines at the point-of-care in less than one week.
Production and secretion of any protein with the desired glycosylation or other post-translational modifications.
In the context of synthesizing materials from engineering biology, this breakthrough capability can include the production and secretion of any small polypeptide, in addition to protein, with the desired modifications, and non-ribosomal protein production. Post-translational modifications that are likely to greatly contribute to protein and polypeptide synthesis for materials include phosphorylation, acetylation, and methylation, among other less-common modifications.
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.
Long-lasting, robust, and low-cost cell-free system for protein synthesis and biomanufacturing.
Identify reagent instabilities in cell-free systems across multiple organisms and all biological kingdoms.
Alleviate reagent instabilities and prolong the half-life of cell-free reagents from a few hours to several days using inexpensive substrates.
Avoid inhibition (poisoning) of cell-free reactions by byproducts or the desired products.
Stabilize catalysts to facilitate cell-free reactions on the order of weeks.
Robust and scalable production of cell-free systems that last for weeks.
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Last updated: January 19, 2021