This is from Codon, my weekly newsletter. Subscribe for free.
☀️ Good morning.
In making war with nature, there was risk of loss in winning.
—John McPhee, “The Control of Nature”
Super Strong Glue, Made from Proteins
An adhesive made from engineered proteins is both biocompatible and biodegradable, achieving an adhesion strength comparable to industrial strength super glue, a new study shows. The work appeared in Nature Communications this week.
How It Works: Elastin is a tough, resilient protein found in extracellular matrices. For this study, the researchers designed peptide sequences, similar to elastin, that contain repeated strings of amino acids: valine-proline-glycine-lysine-glycine. When these repetitive protein sequences are expressed within a cell, such as E. coli, the lysine amino acid in the fourth position is protonated. As the protein grows in length, it becomes increasingly positively charged.
The researchers expressed these repetitive proteins in E. coli (on a plasmid), extracted them, and mixed them with an FDA-approved surfactant used in the cosmetics industry, called sodium dodecylbenzene sulfonate. This surfactant is highly negatively charged. After mixing the two compounds and centrifuging the samples, the researchers scraped off the top layer of liquid and used that as their “biological super glue.”
The team stuck the glue to all kinds of materials — aluminum, glass, steel, PVC. It stuck best to glass, steel and aluminum.
In a further round of experiments, they used the “protein glue” to seal wounds in a pig’s liver, muscle and heart tissues. It stuck well and sealed wounds in every test.
In a final experiment, the team compared the protein glue to both sutures and medical-grade glue by sealing skin wounds in rats. After eight days, the protein glue completely healed the wound and degraded from view. At that time point, the suture and medical glue-sealed wounds were still visible.
Why It Matters: Many adhesives, despite their importance for surgical wound healing, cause skin irritation or don’t stick well to wet tissues. The protein glue, developed by researchers at RWTH Aachen University (Germany) and the Changchun Institute of Applied Chemistry (China), binds strongly even to wet tissues, biodegrades rapidly, and is biocompatible. It can also be made quickly, using recombinant E. coli cells and FDA-approved surfactants, which might expedite its entry to the clinic.
Proteobacteria Engineering Made Easy
A new toolkit of genetic parts — including promoters, terminators and antibiotic resistance cassettes — makes it easy to engineer various proteobacteria strains, a new study shows. The work was published in Nucleic Acids Research this week and was authored by Layla Schuster and Christopher Reisch at the University of Florida in Gainesville.
How It Works: This toolbox includes four different types of parts: origins of replication (which help plasmids to replicate), promoters and their regulator pairs, antibiotic-resistance markers, and seven reporter genes (such as fluorescent proteins). The toolbox has 4 different origins of replication, 12 promoter-regulator pairs, 8 antibiotic resistant genes and 7 reporter genes. Some of the toolbox’s parts were taken from prior research, including the Voigt lab’s Marionette strains.
To join the parts together, each part is first individually amplified, using PCR. As a part is copied by PCR, the primers produce overhang sequences that match the adjacent parts, enabling 4-part plasmids to be created using simple genetic cloning methods.
The researchers tested the toolbox in nine different types of Proteobacteria, including Acinetobacter baylyi (a gram-negative pathogen) and Pseudomonas putida (a gram-negative soil bacterium).
Each promoter in the toolbox is inducible, meaning that genes can be switched on by adding a chemical inducer molecule. The researchers tested every promoter-regulator pair in each of the 9 different bacterial strains, rigorously documenting how well each promoter worked. “In eight bacteria, at least two promoter-regulators were found to have an induction range of over 50-fold,” wrote the researchers. “Surprisingly, commonly used systems derived from E. coli, such as LacI- and TetR-regulated promoters, were not among those with the largest expression ranges in our dataset.”
The researchers tested over 50 plasmids in their study, all of which are available to other scientists.
Why It Matters: I chose to feature this study because toolkits are a useful entry point to strain engineering, and I like that this study tested the toolkit in nine different types of proteobacteria. Even if you don’t use this toolkit, the data presented in the paper offers, perhaps, a useful starting point for engineering various proteobacteria, and for deciding which promoters are best suited for your experiments.
Engineered Nanoparticles Temper Inflammation
Nanoparticles filled with an anti-inflammatory drug, and coated with an engineered protein, can fight inflammation deep in the lungs of mice, a new study shows. The work appeared in Science Advances and was led by researchers at the University of California San Diego.
How It Works: During an inflammatory response, specific proteins appear in copious quantities. One such protein, called vascular cell adhesion molecule-1, or VCAM-1, helps immune cells bind to the inflamed area. As leukocyte cells swarm into the inflamed area, for example, they bind to VCAM-1 by expressing their own protein, called “very late antigen-4,” or VLA-4.
For this study, researchers used genetic engineering to make cells that express VLA-4 and display it on their surface. The scientists then peeled away that cell membrane — and its smattering of proteins — and coated nanoparticles with them. Then, they packed the protein-coated nanoparticles with an anti-inflammatory drug called dexamethasone.
So to summarize: Nanoparticles, filled with dexamethasone, are coated with genetically-engineered cell membranes that are, themselves, coated in VLA-4 proteins. Amazing.
The researchers show that these engineered nanoparticles can sit around in sugar water, cooled to 4 degrees Celsius, for at least 8 weeks without anything happening to them. They also showed, in vitro, that the VLA-4 proteins on the nanoparticles bind strongly to VCAM-1. After further experiments in a cell culture model, the researchers tested their engineered nanoparticles in mice that had been injected with lipopolysaccharides, molecules that cause lung inflammation.
The researchers injected inflamed mice with the nanoparticles, waited 6 hours, and then harvested their organs. The nanoparticles, they found, had accumulated in the liver, spleen and lungs. The nanoparticles completely abrogated lung inflammation, according to the researchers. Mice injected with the nanoparticles also had increased leukocyte recruitment in their lungs.
Why It Matters: This paper is intriguing, I think, because it merges traditional “drug-filled” nanoparticles with genetic engineering. A drug and therapeutic protein, delivered simultaneously, tempered lung inflammation in just 6 hours. I’m also intrigued by the idea that membranes can be stripped from engineered cells and coated onto nanoparticles, much like a mask. That’s pretty cool.
🧫 Other Studies This Week
- (Preprint) Minicells from Highly Genome Reduced Escherichia coli: Cytoplasmic and Surface Expression of Recombinant Proteins and Incorporation in the Minicells. bioRxiv (Open Access). Link
- (Preprint) Shaping liposomes by cell-free expressed bacterial microtubules. bioRxiv (Open Access). Link
- High-throughput screening and rational design of biofunctionalized surfaces with optimized biocompatibility and antimicrobial activity. Nature Communications (Open Access). Link
- Yeast Synthetic Minimal Biosensors for Evaluating Protein Production. ACS Synthetic Biology (Open Access). Link
- (Preprint) Evolving small-molecule biosensors with improved performance and reprogrammed ligand specificity using OrthoRep. bioRxiv (Open Access). Link
- (Review) Genetic Diversity for Accelerating Microbial Adaptive Laboratory Evolution. ACS Synthetic Biology. Link
- Live-cell imaging of circadian clock protein dynamics in CRISPR-generated knock-in cells. Nature Communications (Open Access). Link
- Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II. Nature Chemical Biology. Link
- CRISPR-Associated Primase-Polymerases are implicated in prokaryotic CRISPR-Cas adaptation. Nature Communications (Open Access). Link
- DNA Computing: NOT Logic Gates See the Light. ACS Synthetic Biology. Link
Genetic Engineering & Control
- In-depth assessment of the PAM compatibility and editing activities of Cas9 variants. Nucleic Acids Research (Open Access). Link
- (Review) Engineering molecular translation systems. Cell Systems. Link
- (Preprint) Temperature-Inducible Precision Guided Sterile Insect Technique. bioRxiv (Open Access). Link
Medicine & Diagnostics
- Inclusion of cGAMP within virus-like particle vaccines enhances their immunogenicity. EMBO Reports (Open Access). Link
- Ultrasensitive detection of circulating tumour DNA via deep methylation sequencing aided by machine learning. Nature Biomedical Engineering. Link (Read the news story).
- Recognition of DNA Target Formulations by CRISPR-Cas12a Using a dsDNA Reporter. ACS Synthetic Biology. Link
- (Preprint) Engineered small extracellular vesicles as a FGL1/PD-L1 dual-targeting delivery system for alleviating immune rejection. bioRxiv (Open Access). Link
- Process intensification for the production of yellow fever virus-like particles (VLPs) as potential recombinant vaccine antigen. Biotechnology and Bioengineering. Link
- Engineering cellular metabolite transport for biosynthesis of computationally predicted tropane alkaloid derivatives in yeast. PNAS. Link
- Targeted CHO cell engineering approaches can reduce HCP-related enzymatic degradation and improve mAb product quality. Biotechnology and Bioengineering. Link
- Engineering oxygen-independent biotin biosynthesis in Saccharomyces cerevisiae. Metabolic Engineering. Link
- Streamlined Human Cell-Based Recombinase-Mediated Cassette Exchange Platform Enables Multigene Expression for the Production of Therapeutic Proteins. ACS Synthetic Biology. Link
- Engineering the permeability of Halomonas bluephagenesis enhanced its chassis properties. Metabolic Engineering. Link
- (Review) Systems-level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica. Biotechnology and Bioengineering (Open Access). Link
- (Review) Bacterial microcompartments: tiny organelles with big potential. Current Opinion in Microbiology. Link
- (Review) Microbial Cell Factories for Green Production of Vitamins. Frontiers in Bioengineering and Biotechnology (Open Access). Link
- (Review) Strategies and challenges with the microbial conversion of methanol to high-value chemicals. Biotechnology and Bioengineering. Link
- CRISPR/Cas9-mediated genome editing for wheat grain quality improvement. Plant Biotechnology Journal (Open Access). Link
- Engineering the protein dynamics of an ancestral luciferase. Nature Communications (Open Access). Link
- Reprogramming signal transduction through a designer receptor tyrosine kinase. Communications Biology (Open Access). Link
- Programmable icosahedral shell system for virus trapping. Nature Materials. Link
Systems Biology, Modelling & Quantitative Studies
- CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems. Nucleic Acids Research (Open Access). Link
- (Perspective) Perfect adaptation in biology. Cell Systems. Link
- Physical theory of biological noise buffering by multicomponent phase separation. PNAS. Link
- (Preprint) Emergent properties of coupled bistable switches. bioRxiv (Open Access). Link
- (Preprint) Reconstruction of genome-scale metabolic model for Hansenula polymorpha using RAVEN toolbox. bioRxiv (Open Access). Link
- (Preprint) Spatial dynamics of feedback and feedforward regulation in cell lineages. bioRxiv (Open Access). Link
- (Preprint) A biochemically-realisable relational model of the self-manufacturing cell. bioRxiv (Open Access). Link
Tools & Technology
- (Preprint) OsciDrop: A versatile on-demand droplet generator. bioRxiv (Open Access). Link
- (Preprint) Engineered Bacteria Computationally Solve Chemically Generated 2X2 Maze Problems. bioRxiv (Open Access). Link
- (Perspective) Synthetic Life and the Value of Life. Frontiers in Bioengineering and Biotechnology (Open Access). Link
✨ Around the Web
MINI OPTOGENETICS: Two new optogenetic devices can be implanted entirely beneath the skin on a mouse’s head, are wirelessly powered, and can be programmed in real-time to synchronize neural activity across up to 256 animals. My latest for Spectrum. Link
ON THE FARM: Farmers are debating the benefits, and pitfalls, of genetically-engineered livestock. A nice article on the issue in EMBO Reports. Link
BILL FEARS: A text snippet in a bill, passed by the U.S. Senate, would require the NIH to build security protocols that genome researchers fear could unduly hinder their work. Science. Link
MEAT LAB ETHICS: Some people fear that lab-grown meat, currently being sold in Singapore by the company Eat Just, could eventually lead to a monopolization on sustainable meats and displace business from traditional farmers. The Guardian. Link
PROTEIN PANACEA: Designer proteins, made in a lab (at places like the Institute for Protein Design, at the University of Washington) are being used to develop medicines and vaccines for SARS-CoV-2. Scientific American. Link
Until next time,