Phage Genome Built in Test Tube: Index #19

The T7 bacteriophage genome, which is 40,000 bases in length, was built from 52 unique pieces of DNA.

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☀️ Good morning,

And a happy new year to you. I hope that this newsletter, sent on the first workday of the new year (I know, yuck), will help round in these hopeful days. It includes some of my favorite bits of research and reviews from the last few weeks.

Phage Genome in a Test Tube

A few weeks back, I wrote an article about a brilliant study from Greg Lohman’s lab at New England Biolabs. In PLOS ONE, his group reported that they could “stitch together” 35 unique pieces of DNA, in a single tube. That was a record at the time (as far as I’m aware), but the same team has already shattered that threshold.

In a new preprint, posted to bioRxiv, Lohman’s team assembled the T7 bacteriophage genome, which is 40,000 bases in length, from 52 unique pieces of DNA. The method used by Lohman’s team to build the genome is called Golden Gate Assembly. It works like this: Molecular machines, called proteins, chew up the ends of each DNA piece. The proteins leave behind “sticky” ends, which can then be joined to other pieces with complementary ends. To join the 52 pieces together, the researchers meticulously tested, tweaked, and tuned those sticky ends until they identified an optimal combination. The new study could be a stepping stone towards miniature genomes, built rapidly and by design. bioRxiv (Open Access). Link

A (Partially-Regenerating) Synthetic Cell

A truly synthetic cell—one built from raw, chemical components, but capable of dividing, and repairing, and consuming, and living—is perhaps the holy grail of synthetic biology. But it’s not an easy task, and creating a miniature chemical system that can do any of those things has proven challenging (but is eminently doable, I believe).

For a new study, in Nature Communications, the Maerkl lab built a partially self-regenerating synthetic cell, which was able to sustain protein synthesis from DNA templates for over a day. The authors used the PURE system—a batch of chemicals, essentially, that replicates the interior of a living cell—and managed to regenerate seven different aminoacyl-tRNA synthetases as well as T7 RNA polymerases by tweaking it a bit. It’s a proof-of-principle, to be sure, but the paper is rich with details, mathematical models, and experimental protocols. It seems like a great step towards a fully regenerating synthetic cell. Shout out to the Build-a-Cell team. Nature Communications (Open Access). Link

Every Yeast Gene, Made Inducible

Another impressive advancement, made in recent days, is a preprint that reports “a genome-scale yeast library with inducible expression of individual genes.” In other words, researchers took 5,687 genes in Saccharomyces cerevisiae (the same type of yeast that is used to make breads and beers, on occasion), and made each of them individually inducible, or able to be activated, with a molecule called β-estradiol. That molecule is not normally found in this type of cell, so it doesn’t mess about with their yeast-y metabolisms. To make each gene inducible, the researchers added a specific promoter sequence to each of them, enabling proteins that sense and interact with the molecule to activate their expression. They also added a unique molecular barcode to each gene, meaning that they can perform high-throughput sequencing experiments on these strains.

This study is not just impressive because of the experimental work involved; researchers often figure out what a gene does by deleting it or inducing it. These strains, then, could help researchers better map the functions of yeast genes. A paper from Open Biology, published last year (open access), commented that about 20% of proteins, even in well-studied organisms like yeast, have not been described at all. bioRxiv (Open Access). Link

Biomaterials, Made with Synthetic Biology

I’m a sucker for biomaterials. That may be because I heard Neri Oxman speak, at the University of Iowa, about “death masks” when I was a sophomore in college. 3D-printed materials, with bacteria encased in side, meticulously shaped into masks…what’s not to love?

A new review takes an in-depth look at biomaterials (both living and non-living), and highlights how they can be made with the help of genetic circuits and other synthetic biology tools. The authors discuss how living biosensors, or therapeutic microbes can be embedded inside. The paper is not open access, but you can check out the full text by visiting the link in this Tweet. Nature Reviews Materials. Link.

Super Precise Genome Deletions

Prime editing is like the beefed-up cousin of CRISPR-Cas9. By fusing an “inactive” version of the Cas9 protein (which can bind DNA but won’t cut it) to an engineered reverse transcriptase enzyme, prime editors can be used to insert or delete nucleotides at specific places in the genome, as well as convert one nucleotide to another, without causing double strand breaks.

For a new preprint, researchers from Jay Shendure’s lab at the University of Washington built a modified prime editing system, called PRIME-Del, that can delete specific regions of the genome (ranging from 20 to 700 base pairs) more specifically than what is currently possible with CRISPR/Cas9 and two guide RNAs. They also used PRIME-Del to insert short pieces of DNA into different genome locations. Shendure summarized the paper on Twitter, saying that the new method is more precise because it doesn’t require double strand breaks or non-homologous end joining, is less constrained by PAM sequences, and can be used to perform multiple deletions at a single time. bioRxiv (Open Access). Link

Credit: Ori Toor // Giphy

🧫 Rapid-Fire Highlights

More research & reviews worth your time

When I first heard that Burger King would be rolling out Impossible burgers, I made my first trip to the fast food chain in probably 13 years. It was worth it, too. My experience with that burger made this new review—comparing cell-based and plant-based approaches to making meat—all the more appealing. Nature Communications (Open Access). Link

Volvox are a type of green algae, sensitive to light. They swim around their microcosms and, when their “eyespots” sense light, they quickly shut off their flagella motor and move towards the light. For one of my favorite studies this week, researchers combined a light projector with a microscope to both photograph and control the movement of these cells. They call the (open source!) project DOME, or Dynamic Optical MicroEnvironment. bioRxiv (Open Access). Link

Synthetic cells are inherently versatile. Much like a (very) skilled mechanic could build a car from miscellaneous parts, scattered around a garage, so too could a talented researcher (in the near future) design custom-made artificial cells. Perhaps that researcher could choose the “shell” of a cell, as well as its inner proteins, DNA sequences, and energy sources. A new review (sort of) looks at this speculative future, explaining how artificial cells can be designed to sense a milieu of environmental molecules. Trends in Biotechnology. Link

CRISPR antidotes? A new review from Jennifer Doudna’s group looks at how molecules in the natural world interact with CRISPR-Cas systems to either enhance their function, or block them from working. Nature Chemical Biology. Link

For a new study, researchers created bacterial biofilms that can be controlled with light. By tuning that light, they created gradients of biofilms, of varying thickness. They then made the light-responsive cells mineralize hydroxyapatite, thus creating light-controllable minerals whose location, and density, can be controlled. Cool! Nature Chemical Biology. Link

Sure, researchers can “turn on” a gene by inducing it with light or chemicals. But it’s much more difficult to precisely tune a gene’s expression, so that just the right amount of protein is produced in a cell. For a new study, researchers at Boston University used synthetic transcription factor decoys—”short DNA sequences that can act like a sponge to soak up free transcription factors in the cell”—to regulate the expression of genes in metabolic pathways in E. coli bacteria. As a proof of concept, the team introduced a decoy system that directed metabolic resources towards increased arginine biosynthesis, thus enhancing arginine production 16-fold with this method. And the decoys didn’t mutate, or break, over time! Nucleic Acids Research (Open Access). Link

A new protocol walks through all the steps needed to design your own, custom DNA nanopores. Build large barrels, embedded in the cell membrane, or origami-like pores with custom functions. Nature Protocols. Link

For a new study, researchers randomly introduced genetic mutations in 47 yeast transcription factors and studied how each of those changes affected the cells’ tolerance to alcohol. Could this work prove foundational for designing yeast that can produce beers with a higher alcohol content? Maybe, I don’t know. Let me know if you try! ACS Synthetic Biology. Link

Have a great week. Until Friday,


Bonus Tweet: Want to sequence a genome and figure out its 3D structure at the same time? A new method can do that. Check out this tweet. 👇