2022BBSRC-NSF/BIO: Self-replicating synthetic cells programmed by RNA
Lead Research Organisation:
University of Cambridge
Department Name: Chemical Engineering and Biotechnology
Abstract
For as long as us humans have been aware that there is a clear difference between living and inanimate matter, we have been trying to answer a fundamental question: what makes something alive?
This question has many possible answers, often at odds with each other, but most definitions of life agree on one point: Life should be able to self-replicate. Cell replication indeed underpins some of the most fundamental characteristics of life-forms, such as their ability to evolve, grow, morph, and adapt to their environment.
Having noted how central self-replication is to life, another question naturally emerges: is it possible to build from scratch something that can replicate itself, like a living cell?
Surely, if we could, it would be the first step towards creating new living things from inanimate matter, which would help us understand the principles that may have led to life emerging on planet earth in the first place, and hold dramatic technological potential.
Thanks to an international team of UK and US scientists, combining expertise in nanotechnology, molecular biology, biophysics, and computational science, we will address this fundamental question, attempting to construct synthetic devices that mimic all critical steps of the replication cycle of biological cells: 1) replication of the genetic material, 2) segregation of the genetic material in different parts of the cell, 3) growth of the cell and 4) its division in two offspring cells.
Many researchers have, over the years, worked on this problem, and succeeded in building synthetic systems capable of competing some of these individual steps. However, achieving all of them with the same system remains difficult. One key hurdle is that it is very challenging with synthetic systems to couple the replication of the genetic material with the growth and division of the enclosure that contains it, so that one step triggers the other.
Our approach solves this problem by re-thinking the role of nucleic acids.
In living cells, nucleic acids are predominantly information carriers, with DNA serving as the long-term storage of genetic information and RNA as a substrate to temporarily hold this information while it is used to build proteins. The latter, alongside few other macromolecules (themselves synthesised by protein-based machinery), constitute the main structural elements of the cell.
In our self-replicating synthetic cells, however, nucleic acids (DNA and RNA) will play BOTH genetic AND structural roles. Our "synthetic cells" will be made primarily out of synthetic RNA nanostructures produced from a DNA genetic code. The RNA nanostructures will be designed to form cell-like devices capable of growing and dividing, as more RNA is produced from DNA, hence establishing a strong connection between genetic and structural replication, which was missing in previous attempts.
By building these nucleic-acid-based, self-replicating synthetic cells, we will not only be able to gauge our ability to imitate life forms and answer questions relative to the origin of life, but we will also pave the way to game-changing technological applications. Synthetic cells constructed from the "bottom-up" are indeed regarded as potentially very valuable in diagnostics and therapeutics, whereby these programmable devices could operate in the body, recognise the presence of a disease, and efficiently tackle it by locally producing and releasing therapeutic payloads. The ability to self-replicate (in a controlled and safe manner) would be crucial for extending the lifespan of the devices, and thus the efficacy of their therapeutic action to the point that it could rival that of cutting-edge therapies based on reprogrammed biological cells.
This question has many possible answers, often at odds with each other, but most definitions of life agree on one point: Life should be able to self-replicate. Cell replication indeed underpins some of the most fundamental characteristics of life-forms, such as their ability to evolve, grow, morph, and adapt to their environment.
Having noted how central self-replication is to life, another question naturally emerges: is it possible to build from scratch something that can replicate itself, like a living cell?
Surely, if we could, it would be the first step towards creating new living things from inanimate matter, which would help us understand the principles that may have led to life emerging on planet earth in the first place, and hold dramatic technological potential.
Thanks to an international team of UK and US scientists, combining expertise in nanotechnology, molecular biology, biophysics, and computational science, we will address this fundamental question, attempting to construct synthetic devices that mimic all critical steps of the replication cycle of biological cells: 1) replication of the genetic material, 2) segregation of the genetic material in different parts of the cell, 3) growth of the cell and 4) its division in two offspring cells.
Many researchers have, over the years, worked on this problem, and succeeded in building synthetic systems capable of competing some of these individual steps. However, achieving all of them with the same system remains difficult. One key hurdle is that it is very challenging with synthetic systems to couple the replication of the genetic material with the growth and division of the enclosure that contains it, so that one step triggers the other.
Our approach solves this problem by re-thinking the role of nucleic acids.
In living cells, nucleic acids are predominantly information carriers, with DNA serving as the long-term storage of genetic information and RNA as a substrate to temporarily hold this information while it is used to build proteins. The latter, alongside few other macromolecules (themselves synthesised by protein-based machinery), constitute the main structural elements of the cell.
In our self-replicating synthetic cells, however, nucleic acids (DNA and RNA) will play BOTH genetic AND structural roles. Our "synthetic cells" will be made primarily out of synthetic RNA nanostructures produced from a DNA genetic code. The RNA nanostructures will be designed to form cell-like devices capable of growing and dividing, as more RNA is produced from DNA, hence establishing a strong connection between genetic and structural replication, which was missing in previous attempts.
By building these nucleic-acid-based, self-replicating synthetic cells, we will not only be able to gauge our ability to imitate life forms and answer questions relative to the origin of life, but we will also pave the way to game-changing technological applications. Synthetic cells constructed from the "bottom-up" are indeed regarded as potentially very valuable in diagnostics and therapeutics, whereby these programmable devices could operate in the body, recognise the presence of a disease, and efficiently tackle it by locally producing and releasing therapeutic payloads. The ability to self-replicate (in a controlled and safe manner) would be crucial for extending the lifespan of the devices, and thus the efficacy of their therapeutic action to the point that it could rival that of cutting-edge therapies based on reprogrammed biological cells.
Technical Summary
Bottom-up synthetic biology aspires to mimic life-like behaviours of biological cells in minimal systems constructed from molecular components: synthetic cells. These devices promise to revolutionise the bio-technological landscape in sectors as diverse as healthcare and biomanufacturing, while offering opportunities to tackle biological questions through a "learning-by-building" approach, including in origin-of-life research.
One of the defining characteristics of biological cells is their ability to grow and divide. The bottom-up construction of synthetic cells featuring these abilities would bring us one step closer to the goal of "creating new life" and benefit those applications that require long term survival of synthetic cells. Cell replication broadly involves four distinct processes: i) genome duplication ii) genome segregation, iii) cell growth and iv) cell division. While, taken individually, these steps have been demonstrated in various synthetic-cell implementations, integrating them all in the same artificial device remains elusive.
With this project, we address this key bottleneck with a solution that that dovetails the toolkit of nucleic-acid nanotechnology with principles of molecular biology, biophysics, and bio-membrane engineering, and leverages state-of-the-art experimental and computational techniques. The synthetic cells will form and grow from RNA building blocks transcribed from a DNA "genome". Division and genome segregation will result from phase separation, while genome replication will be underpinned by reverse transcription. The synthetic cells will be able to operate with or without a lipid membrane. Because the nucleic-acid nanostructures will play, at the same time, structural and genetic roles, the sought synergy between genetic replication, segregation, compartment growth and division will naturally emerge, making our devices the first synthetic cell implementation capable of supporting all key stages of cell replication.
One of the defining characteristics of biological cells is their ability to grow and divide. The bottom-up construction of synthetic cells featuring these abilities would bring us one step closer to the goal of "creating new life" and benefit those applications that require long term survival of synthetic cells. Cell replication broadly involves four distinct processes: i) genome duplication ii) genome segregation, iii) cell growth and iv) cell division. While, taken individually, these steps have been demonstrated in various synthetic-cell implementations, integrating them all in the same artificial device remains elusive.
With this project, we address this key bottleneck with a solution that that dovetails the toolkit of nucleic-acid nanotechnology with principles of molecular biology, biophysics, and bio-membrane engineering, and leverages state-of-the-art experimental and computational techniques. The synthetic cells will form and grow from RNA building blocks transcribed from a DNA "genome". Division and genome segregation will result from phase separation, while genome replication will be underpinned by reverse transcription. The synthetic cells will be able to operate with or without a lipid membrane. Because the nucleic-acid nanostructures will play, at the same time, structural and genetic roles, the sought synergy between genetic replication, segregation, compartment growth and division will naturally emerge, making our devices the first synthetic cell implementation capable of supporting all key stages of cell replication.
