A group of chemists from multiple universities, led by the University of California, Berkeley, is aiming to revolutionize the capabilities of cell-based manufacturing. While synthetic biologists have already made significant progress in using microbes to produce various chemicals, this research enterprise seeks to reprogram the cell’s ribosomes, the molecular machines responsible for protein synthesis, to create more complex and elaborate polymer chains.
In a series of papers published in Nature Chemistry and ACS Central Science, the researchers address three major challenges: reprogramming cells to supply the ribosomes with building blocks other than the standard alpha-amino acids, determining the most suitable building blocks for the ribosome, and modifying the ribosome to incorporate these novel building blocks into polymers.
The long-term objective of the National Science Foundation Center for Genetically Encoded Materials (C-GEM) is to develop a fully programmable translation system. This would allow researchers to introduce mRNA instructions and new building blocks into the cell, enabling the ribosome to produce an extensive array of novel molecular chains. These chains could serve as the foundation for groundbreaking bio-materials, enzymes, and pharmaceuticals.
The successful implementation of this project would grant polymer chemists, medicinal chemists, and biomaterials scientists the tools to create custom materials with unique functions. The reengineered cellular machinery would facilitate the biosynthesis of previously unattainable molecules, with specific applications and properties. For instance, it could enable the production of polymer hybrids combining the toughness of spider silk with the versatility of nylon. The technology could also yield heat-resistant protein-like polymers that surpass the capabilities of naturally occurring proteins.
An essential aspect of a programmable ribosome machine capable of synthesizing polymers is its potential for evolutionary optimization. Just as proteins have evolved over millions of years, these polymers could undergo directed evolution to enhance their activity and functionality. This represents a significant advancement beyond the directed evolution of protein enzymes for which Frances Arnold received the 2018 Nobel Prize in Chemistry.
By establishing a system that allows for the evolution of polymers never before observed in nature, researchers hope to create a platform for the development of tailored polymers based on individual creative ideas. This groundbreaking technology could unlock a new realm of possibilities in material science and pharmaceutical research.
Engineering an entirely new ribosome
Proteins are essential components of cells, synthesized by ribosomes based on instructions from messenger RNA (mRNA). The ribosome reads the mRNA and assembles the protein by linking amino acids together in a specific order. These proteins then fold into unique 3D structures, enabling them to perform various functions in the cell.
Initially, reprogramming the ribosome seemed like an impossible task, but the National Science Foundation Center for Genetically Encoded Materials (C-GEM) was established to pursue this goal. C-GEM aims to expand the ribosome’s capabilities by introducing alternative building blocks, called monomers, instead of the standard alpha-amino acids. To achieve this, the researchers focused on the enzymes responsible for loading amino acid monomers onto transfer RNA (tRNA), which transports them to the ribosome.
In a recent paper published in Nature Chemistry, the C-GEM team discovered a family of tRNA synthetases capable of loading tRNA with four different non-alpha-amino acids, including a precursor used in the synthesis of polyketide therapeutics like erythromycin and tetracycline. This finding opens up possibilities for generating novel molecules with unique functions, which could contribute to addressing the problem of antibiotic resistance.
In another paper published in ACS Central Science, the researchers used cryogenic electron microscopy (cryo-EM) to study the binding of three non-alpha-amino acid monomers to the E. coli ribosome. This provided insights into how these monomers interact with the ribosome and suggestions for improving their binding efficiency.
A third paper, also in Nature Chemistry, focused on the cryo-EM structure of the E. coli ribosome while binding normal alpha-amino acids. Computational modeling was employed to understand which non-natural monomers could react in the ribosome’s catalytic center, known as the peptidyl transferase center (PTC).
Throughout these studies, the researchers emphasized the need for the ribosomal system to function within a living cell, independently of the normal ribosomes. This ensures that the production of new polymers does not interfere with the essential protein synthesis processes required for cellular function and life.
The researchers acknowledge the challenges involved in developing robust ribosomes and enzymes for scalable applications within cells. However, they find the work exciting and valuable for educating and involving students and postdocs in cutting-edge scientific research.