From Mammoths to Materials: Synthetic Biology Moves Into The

Biomaterials From mammoths to materials: synthetic biology moves into

the biomaterial space Downloaded from http://portlandpress.com/biochemist/article-pdf/40/1/20/851832/bio040010020.pdf by guest on 25 September 2021

Michael R. Behrens and Synthetic biology is a relatively new research field that employs synthetic recombinant DNA Warren C. Ruder technologies to engineer capabilities for addressing a wide variety of scientific and societal (University of Pittsburgh, USA) problems. We highlight a few noteworthy projects and achievements spanning the field of synthetic biology. In particular, some of the ways synthetic biological tools have been used to create novel biomaterials. Biological systems, like cells or larger organisms, can be made not only to synthesize new biomaterials but also to act as biomaterial constituents themselves, imbuing the materials with useful biological properties like the ability to respond dynamically to environmental cues. Looking into the future, there are many promising research directions synthetic biologists can take to develop tomorrow’s biomaterials.

Synthetic biology can mean many things to many people, In a proof of principle experiment, Venter’s team but there is a uniting thread running through every outsourced the production of the entire project assuming that name. Driven by the dramatic genome of Mycoplasma mycoides, reduction in cost of gene synthesis over the last two ordered in bite-size chunks decades – approximately two orders of magnitude – the from commercial DNA field of synthetic biology could be broadly described as sequencing services, the use of recombinant and synthetic DNA technologies which they to create new biological products, organisms and subsequently systems unseen in nature. Within this broad definition, reassembled in numerous and diverse fields of research have arisen, the lab. They ranging from the resurrection of long-dead giants to the then took production of new biomaterials for tissue engineering. the native Synthetic biology is a discipline that is seemingly bounded only by the creativity of its practitioners. Some of the most newsworthy projects in synthetic biology involve creating new organisms, modifying existing ones or resurrecting extinct species. For example, a team led by George Church at Harvard is working to bring back the woolly mammoth. To do so, they are starting with the genome of the Asian elephant and, informed by sequencing projects, are selectively removing ‘elephant-specific’ genes and introducing ‘mammoth’ genes in order to convert the elephant step-by-step into its long-lost Arctic cousin. In a separate project, exploiting similar techniques to manipulate the DNA, synthetic biologists at the University of Japan are aiming to produce hypoallergenic glow-in-the-dark cats, which may become the must-have pet of the near future. In 2010, Craig Venter and colleagues grabbed the headlines when they introduced the world to Mycoplasma laboratorium, better known as Synthia.

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chromosome out of the cell of a related species metabolic pathways. For example, at the University of Mycoplasma capricolum, and replaced it with the fully California at Berkeley, a team of synthetic biologists synthesized M. mycoides genome (including a couple of led by Jay Keasling has engineered yeast to produce additional signature sequences to make it distinguishable artemisinic acid, a precursor to the antimalarial drug from the original). This new cell grew successfully. artemisinin. A fermentation plant built by the French Why take this convoluted route to produce a slightly pharmaceutical giant Sanofi has the capacity to produce altered bacterium? The intention is to identify a cell about 60 tons per year of this synthetic artemisinic with the minimal genome to sustain life, a chassis, into acid, meeting approximately one-third of the global which other genes can then be selectively introduced demand. Synthetic artemisinin based on this biological to produce organisms that fulfil designated functions. breakthrough entered the market in 2014, and in 2016 Scientists engaged in this type of work hypothesize that about 10% of the global demand for artemisinin-based by removing all of the unnecessary activities of the cell, antimalarial treatments was met through synthetic Downloaded from http://portlandpress.com/biochemist/article-pdf/40/1/20/851832/bio040010020.pdf by guest on 25 September 2021 and then adding genetic circuitry designed to cause the artemisinin production. cell to produce large quantities of specific chemicals, more cellular energy and resources can be focused Synbio enters the biomaterials space on the production of desired metabolites, driving up production efficiency. As a field with such diversity, spanning from mammoths There is good reason to want to develop chassis to medicine, it is not surprising that synthetic biology organisms for metabolic engineering, since some of has also turned its tools and methods towards the the greatest commercial successes of synthetic biology production of new biomaterials. The goal of many to date have been the production of high-value biomaterials researchers is to create materials that chemicals through the rewiring of cellular as closely as possible mimic the natural materials found inside living organisms. For example, in lieu of natural human extracellular matrix for tissue engineering applications, synthetic biomaterials such as poly(lactic-co-glycolic acid) or hyaluronic acid are used in tissue engineering as growth substrates for cells, mimicking properties of the natural matrix. Natural protein-based extracellular matrix for tissue

engineering may be obtained from animal sources, but immune reactions and the rejection of foreign biological material may pose problems when it is time to seed human cells onto the matrix, or transplant the new tissue into a patient. Collagen is one such matrix protein that has been taken from animals for use as a tissue scaffold. But since animal-based transplants can often be rejected, is there a way we can use synthetic biology to solve this

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problem? Since collagen is a protein-based polymer, it pattern of monomers dictated by the researchers. By is created through the instructions encoded into genes, adding genes for monomers that had extra protein with ribosomes faithfully assembling it one amino motifs added to them that bind to nickel atoms, acid at a time. The critical differences between human and then mixing nickel and gold nanoparticles with collagen and bovine collagen, which are a result of our the cells, the researchers were able to create precise divergent evolutionary history, manifest as slightly patterns of conducting nanowires, all through the altered protein amino acid sequences or motifs. With power of genetic engineering. synthetic biological tools, we can alter these motifs, But the story doesn’t end there. With synthetic effectively camouflaging the non-native collagen so that biology, it is also possible to induce the cells to the immune system sees it as ‘self’. It is even possible to synthesize the metallic nanoparticles themselves. create new sources of collagen by expressing the human Metallic nanoparticles have found many uses in

collagen genes in yeast, growing them in huge vats and biological research and medicine, including targeted Downloaded from http://portlandpress.com/biochemist/article-pdf/40/1/20/851832/bio040010020.pdf by guest on 25 September 2021 purifying the collagen for use as a material. But we can go drug delivery, use as fluorescent markers, and contrast a step further than merely mimicking human collagen, agents for ultrasound and magnetic resonance imaging. we could even alter the genetic sequence to create custom Cells have also developed their own uses for metallic protein-based polymers with new properties for specific nanoparticles, such as magnetotactic bacteria, which tissue-engineering applications that natural collagen is synthesize magnetic nanoparticles of iron oxide in not suitable for. Proteins are programmable materials, so order to orient themselves along the earth’s magnetic let’s get to work and start writing new programs! field, which allows them to efficiently search their environment for food. In order to capitalize on this Programming biology ability and to make a diverse range of nanoparticles through biological means, researchers in Sang Yup Programming biological polymers for custom Lee’s lab at the Korea Advanced Institute of Science applications is the goal of scientists in the lab of Timothy and Technology have developed a synthetic genetic Lu at the Massachusetts Institute of Technology. circuit that can be added to bacteria in order to They are using bacterial curli amyloid fibres as a synthesize nanoparticles out of metal ions in solution. model system. Bacteria naturally use these fibres as By adding two recombinant metal-chelating proteins, an extracellular matrix for the formation of biofilms phytochelatin (PC) and metallothionein (MT), to and attachment to surfaces in their environment. Escherichia coli cells and then by varying the ratios The fibres are produced by the sequential assembly and combinations of metals in the growth media, of monomer units called CsgA. Lu’s team replaced numerous types of nanoparticles were formed within the native curli-forming system in the bacteria the cells with controllable size and stoichiometry. with one that can be controllably expressed when With this technology, they have demonstrated the the researchers give the bacteria particular signals, ability to grow a variety of particle types, including essentially transferring control of the assembly process magnetic, noble metal, semiconductor and alkali- from the bacteria to the scientists. Then, they started earth metal, all of which could be used as biomaterials to play with the assembly process. Genes for multiple for various downstream applications. monomers of CsgA, all with different properties programmed into their DNA sequences, were added Future directions to the cells, all under the control of different external signals. This way, by setting up a pattern over time of What does the future hold for synthetic biology? different external signals, the scientists could control What new biomaterials can be created through these which monomers the cells were producing, and when. powerful technologies? We believe that in the future, This could then be used to tune the precise properties synthetic biology could be used to create not just of the polymer, as the chains are assembled with a materials to interface with living systems, but that

the materials could themselves be living systems. Michael Behrens is a PhD student at Cells are dynamic, complex, and to a synthetic the University of Pittsburgh in the biologist, reprogrammable biological computational Department of Bioengineering, where units. By integrating engineered cells as structural he works in the group of Dr Warren components of biomaterials, the materials could Ruder. He received his BS in Electrical be imbued with these properties. Environmental Engineering from Walla Walla University cues could be integrated and processed by the in 2016. His research focuses on employing synthetic biology cells, which could take this information and use it for biomaterials and tissue engineering applications. Email: to dynamically remodel the biomaterial in order to [email protected]. adapt to the new conditions. Rather than passive biomaterials that must be designed to operate in a specific environment, a living, sensing, computing Downloaded from http://portlandpress.com/biochemist/article-pdf/40/1/20/851832/bio040010020.pdf by guest on 25 September 2021 material could be designed to function optimally in Dr Warren Ruder is an Assistant many environments, even changing its properties Professor at the University of Pittsburgh at the behest of the engineers creating it. If cells are in the Department of Bioengineering, not integrated directly into the material, they could where he runs the Engineered Living still be programmed to interact with biomaterials in Systems Laboratory. His expertise is in new ways. Cells produce adhesion proteins called synthetic biology, cellular and molecular integrins, which will bind to a specific peptide biomechanics, and lab-on-a-chip systems. His research group sequence, arginine-glycine-aspartic acid (RGD). explores the synthetic biological design space, from using This sequence is often integrated into synthetic genetic circuitry for reprogramming surface chemistry, all the biomaterial polymers in order to control the way to hybrid living robotic models of the gut–brain axis. Dr interaction of the material with the cells. But what Ruder received his PhD in Biomedical Engineering from Carnegie if the cells could also be programmed to control Mellon University. Email: [email protected]. their interaction with the material? With synthetic biology, both sides of the material–cell interface are available for engineers to control. Imagine if cells Additional reading to be incorporated into a synthetic tissue could be engineered to change the way they express integrins. • Chen, A.Y., Deng, Z., Billings, A.N. et al. (2014) Perhaps under certain conditions the cells need to Synthesis and patterning of tunable multiscale adhere strongly to the material, and under other materials with engineered cells. Nature Materials conditions they need to let go. With traditional 13, 515 biomaterials, this type of interaction is largely out of • Hutchison, C.A., Chuang, R-Y., Noskov, V.N., et al. the hands of the engineer, and the material is static (2016) Design and synthesis of a minimal bacterial once formed and integrated into the tissue. But with genome. Science 351(6280) synthetic biology, we could program the behaviour of • Paddon, C.J. and Keasling, J.D. (2014) Semi-synthetic the cells by controlling their expression of integrins, artemisinin: a model for the use of synthetic biology dynamically changing their relationship to the in pharmaceutical development. Nature Reviews biomaterials they interact with. Add more integrins, Microbiology 12, 355 take more out, do so dynamically under the control • Park, T.J., Lee, S.Y., Heo, N.H. and Seo, T.S. (2010) In of environmental cues to remodel the tissue… all vivo synthesis of diverse metal nanoparticles by could be possible with synthetic biology. Watch this recombinant Escherichia coli. Angewandte Chemie space; synthetic biology is positioned to dramatically International Edition 49(39), 7019–7024 change the way we think about biomaterial design • Wong Po Foo, C. and D.L. Kaplan (2002) Genetic and tissue engineering. ■ engineering of fibrous proteins: spider dragline silk and collagen. Adv. Drug Deliv. Rev. 54(8), 1131–1143 • Wongsrikeao, P., Saenz, D., Rinkoski, T., Otoi, T. and Poeschla, E. (2011) Antiviral restriction factor transgenesis in the domestic cat. Nature Methods 8(10), 853–859 • Worrall, S. (2017) We could resurrect the woolly mammoth. Here’s how. National Geographic. https:// news.nationalgeographic.com/2017/07/woolly- mammoths-extinction-cloning-genetics/