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☀️ Good morning.
It starts at the bottom, viewing an organism as a large population of simple machines, and works upwards synthetically from there — constructing large aggregates of simple, rule-governed objects which interact with one another nonlinearly in the support of life-like, global dynamics. The ‘key' concept in [artificial life] is emergent behavior.
—Christopher Langton in the book “Artificial Life,” 1989
Smart Watch Triggers Therapeutic Transgene
When wearable devices meet synthetic biology, you have a recipe for Silicon Valley success. That might be the case, at least, for a new study published this week in Nature Communications: researchers used the green LED on an Apple Watch — which is normally used to track heart rate, blood pressure and sleep patterns — to trigger the release of a therapeutic protein in human cells.
How It Works: The study begins with T. thermophilus, extremophile bacteria that can grow at 82°C. These bacteria have a protein called carH that silences genes involved in carotenoid biosynthesis. CarH is a homotetramer (a protein complex made up of four identical subunits) that, when exposed to light, breaks up into monomers. CarH requires a coenzyme, vitamin B12, to function properly.
For this study, researchers took the vitamin B12-subunit from carH and fused it to a synthetic transcription factor. Without light, carH holds the transcription factor closely, blocking it from switching on genes. But when a cell is blasted with light, carH falls apart and the transcription factor is released. That released transcription factor then parades through the cell and switches on a gene.
In this paper, the researchers — led by Martin Fussenegger at ETH Zurich, Switzerland — engineered carH to switch on a gene, specifically, that encodes glucagon-like peptide-1, a protein that inhibits glucagon release and lowers blood sugar levels. They called their system Glow Control (green-light-operated smart-watch control system).
The team implanted mice with 10 million HEK293T cells that had been engineered to express carH and the synthetic transcription factor. Then, they strapped an Apple Watch to the backs of those mice.
When the team switched on the Apple Watch’s green light, the HEK293T cells responded by releasing glucagon-like peptide-1 in the animals. Mice with the therapeutic transgene + Apple Watch had reduced blood glucose levels and lost weight after 12 days.
Why It Matters: Apple fans probably won’t be engineered with therapeutic transgenes any time soon. But this paper is still intriguing because it shows that synthetic biology can be interfaced with electronic devices. Perhaps engineered bacteria, embedded into clothing, could similarly be activated with a smart watch to produce molecules on-demand.
Evolved Protein Capsid Packs Its Own RNA Encoding Sequence
Viruses are biological wonders. Dozens or hundreds of proteins come together and join hands, enclosing a piece of DNA or RNA that encodes more of those proteins. It’s a molecular dance that has evolved over billions of years.
Now, researchers have managed to evolve proteins, in the laboratory, that can form “virus-like capsids” that take up and store RNA molecules encoding more of their own proteins.
How It Works: For the new study, in Science, the researchers evolved a nucleocapsid protein from Aquifex aeolicus. This protein naturally forms nanocontainers, comprised of 60 individual subunits, but does not recognize nucleic acids.
The team, led by Donald Hilvert’s group at ETH Zurich, Switzerland, attached an arginine-rich peptide to the aeolicus protein (this peptide recognizes, and binds, an RNA stem-loop motif called BoxB) and then used directed evolution. 1-in-8 of the evolved proteins with the arginine-rich peptide could capture mRNA transcripts flanked by BoxB tags.
To improve their design, the team next used error-prone PCR to mutagenize the gene encoding their evolved protein. As they mutagenized the DNA, the proteins got smaller and smaller, but also got better and better at recognizing the RNA’s BoxB motifs. The best variant, write the researchers, “had nine new mutations.” The evolved proteins, in the end, formed 240-subunit icosahedral capsids that could take up and encapsulate their own encoding RNA sequence 64 percent of the time. That is a vast improvement compared to prior “virus-like capsids” made by synthetic biologists.
Why It Matters: By engineering and then evolving proteins to form nucleocapsids that can take up their own encoding RNA sequences, researchers can better study how viruses evolve naturally. Scientists can also use these techniques, potentially, to improve nanocages for drug delivery.
Minimal Genomes, Simulated
Mycoplasma genitalium is a bacterium with just 538 genes, 482 of which are protein-coding. It has the smallest genome of any known, free-living organism.
Due to its small stature, M. genitalium is a convenient “starting point” to identify the minimal set of genes necessary for life. The J. Craig Venter Institute has already made progress on that front; their synthetic M. genitalium organism, from 2016, has just 473 genes.
Unfortunately, building minimal genomes in the lab takes a long time. To speed up the process, researchers often use in silico, computational models to predict which subset of genes from M. genitalium are required for life.
For a new study in ACS Synthetic Biology, researchers led by Lucia Marucci and Claire Grierson’s groups at the University of Bristol, England, tested ten different “minimal gene sets” for M. genitalium using a computational, whole-cell model.
How It Works: The ten gene sets ranged vastly in size; the smallest “theoretical genome,” designed by Anthony Forster and George Church in 2006, has just 89 genes. The largest gene sets, from the Venter Institute, have more than 250 genes.
The researchers ran computational simulations on each of the gene sets using Markus Covert’s freely-available whole-cell model. They found that none of the gene sets, as described, could produce viable cells.
So the researchers, in this study, began adding back genes to each of the 10 sets. Eventually, they were able to make “minimal” cells divide in their simulations. The smallest viable “theoretical” genome had 259 genes, which is quite similar to predictions from the Venter Institute nearly two decades ago.
Why It Matters: This study is entirely computational, and a slew of experiments are needed to determine the smallest genome required for a functional, dividing cell. This study is intriguing, though, because it shines a light on the rapid biological advancements that have taken place in the last decade.
All of the theoretical genomes that this paper simulated were introduced in 2013 or earlier. As such, all of the gene sets had inadvertently discarded genes that scientists now know to be essential, including genes for chromosome segregation and glycine production. As biology advances in fundamental ways, so too will synthetic biology.
🧫 Other Studies This Week
- Dynamic self-assembly of compartmentalized DNA nanotubes. Nature Communications (Open Access). Link
- Living fabrication of functional semi-interpenetrating polymeric materials. Nature Communications (Open Access). Link
- Microbial whole-cell biosensors: Current applications, challenges, and future perspectives. Biosensors and Bioelectronics. Link
- A synthetic RNA-mediated evolution system in yeast. Nucleic Acids Research (Open Access). Link
- (Perspective) Towards an engineering theory of evolution. Nature Communications (Open Access). Link
- Promiscuous molecules for smarter file operations in DNA-based data storage. Nature Communications (Open Access). Link
- Defining genome architecture at base-pair resolution. Nature. Link
- A genome-scale yeast library with inducible expression of individual genes. Molecular Systems Biology (Open Access). Link
- (Preprint) Genetically engineered insects with sex-selection and genetic incompatibility enable population suppression. bioRxiv (Open Access). Link
Genetic Engineering & Control
- (Preprint) Scalable and Automated CRISPR-Based Strain Engineering Using Droplet Microfluidics. bioRxiv (Open Access). Link
- Enzymatic Synthesis of Chimeric DNA Oligonucleotides by in Vitro Transcription with dTTP, dCTP, dATP, and 2′-Fluoro Modified dGTP. ACS Synthetic Biology. Link
- Designing an irreversible metabolic switch for scalable induction of microbial chemical production. Nature Communications (Open Access). Link
- Design of Synthetic Quorum Sensing Achieving Induction Timing-Independent Signal Stabilization for Dynamic Metabolic Engineering of E. coli. ACS Synthetic Biology. Link
- Production of the infant formula ingredient 1,3-olein-2-palmitin in Arabidopsis thaliana seeds. Metabolic Engineering. Link
- (Preprint) Using structurally fungible biosensors to evolve improved alkaloid biosyntheses. bioRxiv (Open Access). Link
- (Preprint) Biosynthesis of cannabinoid precursor olivetolic acid by overcoming rate-limiting steps in genetically engineered Yarrowia lipolytica. bioRxiv (Open Access). Link
- Development of a growth coupled and multi-layered dynamic regulation network balancing malonyl-CoA node to enhance (2S)-naringenin biosynthesis in Escherichia coli. Metabolic Engineering. Link
- Combining Metabolic and Monoterpene Synthase Engineering for de Novo Production of Monoterpene Alcohols in Escherichia coli. ACS Synthetic Biology. Link
- High-Yielding Terpene-Based Biofuel Production in Rhodobacter capsulatus. ACS Synthetic Biology. Link
- Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties. Metabolic Engineering. Link
- Construction of DNA Tools for Hyperexpression in Marchantia Chloroplasts. ACS Synthetic Biology (Open Access). Link
- (Preprint) Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. bioRxiv (Open Access). Link
- (Preprint) A light tunable differentiation system for the creation and control of consortia in yeast. bioRxiv (Open Access). Link
- Engineered bridge protein with dual affinity for bone morphogenetic protein-2 and collagen enhances bone regeneration for spinal fusion. Science Advances (Open Access). Link
Systems Biology, Modelling & Quantitative Studies
- Comparative analysis of three studies measuring fluorescence from engineered bacterial genetic constructs. PLOS ONE (Open Access). Link
- (Preprint) Distinguishing between models of mammalian gene expression: telegraph-like models versus mechanistic models. bioRxiv (Open Access). Link
- (Preprint) Characterizing non-exponential growth and bimodal cell size distributions in Schizosaccharomyces pombe: an analytical approach. bioRxiv (Open Access). Link
- (Preprint) The acquisition of additional feedback loops may optimize and speed up the response of quorum sensing. bioRxiv (Open Access). Link
- (Preprint) Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies. bioRxiv (Open Access). Link
- (Preprint) Global dynamics of microbial communities emerge from local interaction rules. bioRxiv (Open Access). Link
- (Preprint) Monod model is insufficient to explain biomass growth in nitrogen-limited yeast fermentation. bioRxiv (Open Access). Link
Tools & Technology
- Rational gRNA Design Based on Transcription Factor Binding Data. Synthetic Biology (Open Access). Link
- (Review) Optical control of targeted protein degradation. Cell Chemical Biology. Link
- (Review) Genome editor-directed in vivo library diversification. Cell Chemical Biology. Link
- Cas9 targeted enrichment of mobile elements using nanopore sequencing. Nature Communications (Open Access). Link
- Imaging of native transcription and transcriptional dynamics in vivo using a tagged Argonaute protein. Nucleic Acids Research (Open Access). Link
- Optoregulated force application to cellular receptors using molecular motors. Nature Communications (Open Access). Link
- (Perspective) The emerging landscape of single-molecule protein sequencing technologies. Nature Methods (Open Access). Link
- (Preprint) Komagataeibacter tool kit (KTK): a modular cloning system for multigene constructs and programmed protein secretion from cellulose producing bacteria. bioRxiv (Open Access). Link
- (Review) Biotechnology for secure biocontainment designs in an emerging bioeconomy. Current Opinion in Biotechnology (Open Access). Link
- (Review) Bioinformational trends in grape and wine biotechnology. Trends in Biotechnology (Open Access). Link
- (Preprint) Provenance Attestation of Human Cells Using Physical Unclonable Functions. bioRxiv (Open Access). Link
✨ Around the Web
GENE SILENCER: A new CRISPR tool can alter the epigenome of human cells, switching off gene expression for months. Spectrum. Link
BIOTECH’S FUTURE: What’s next for biotech? George Church has a lot of predictions, from carbon sequestration to array synthesis for creating new enzymes en masse. Nature Biotechnology. Link
HOPPIN’ DNA: Horizontal gene transfer is happening in vertebrates, and scientists don’t always understand why. Quanta Magazine. Link
SYNTHETIC CYTOKINES: A company called Synthekine is engineering cytokines to be more specific, thus reducing therapeutic side effects. Nature Biotechnology. Link
SWISS STARTUPS: Swiss biotechnology startups are booming. This article lays out the landscape. Labiotech.eu. Link
PRIME PLANTS: The efficiency and specificity of prime editors are swiftly improving in plants, thanks in part to Caixia Gao’s lab at the Chinese Academy of Sciences. Nature. Link
JOB: Empress Therapeutics are hiring a synthetic biologist for their headquarters in Cambridge, Mass. Apply here.
Until next time,