Phage Genome in a Test Tube

Recently, I discussed a remarkable study from Greg Lohman’s team at New England Biolabs. Their work, published in PLOS ONE, showcased their ability to “stitch together” 35 distinct DNA fragments within a single tube, setting a new record. This impressive feat has already been surpassed in a new preprint on bioRxiv, where the team successfully assembled the T7 bacteriophage genome, comprising 40,000 bases from 52 unique DNA segments. The innovative method they utilized is known as Golden Gate Assembly. Here’s how it functions: Proteins, which act as molecular machines, digest the ends of each DNA fragment, leaving behind “sticky” ends that can bond with complementary sequences. The researchers meticulously experimented with these sticky ends, optimizing the combination needed to join all 52 segments. This advancement paves the way for the rapid assembly of miniature genomes designed with precision.

A (Partially-Regenerating) Synthetic Cell

The quest for a fully synthetic cell, constructed from basic chemical components yet capable of self-replication, repair, and sustenance, remains a pinnacle of synthetic biology. Achieving this is challenging, yet feasible. In a recent study published in Nature Communications, the Maerkl lab developed a partially self-regenerating synthetic cell that maintained protein synthesis from DNA templates for over 24 hours. They employed the PURE system, which simulates the interior of a living cell, to regenerate seven different aminoacyl-tRNA synthetases alongside T7 RNA polymerases through slight modifications. This proof-of-concept study is rich in experimental details and mathematical models, representing a significant step toward creating fully regenerating synthetic cells.

Every Yeast Gene, Made Inducible

An exciting breakthrough emerged recently with a preprint detailing the creation of a genome-wide yeast library that allows for the inducible expression of individual genes. Researchers have modified 5,687 genes in Saccharomyces cerevisiae, the yeast commonly used in baking and brewing, to be activated by a molecule called ?-estradiol, which is not typically present in these cells, ensuring no disruption of their metabolic processes. By incorporating a specific promoter sequence into each gene, the researchers enabled proteins that interact with ?-estradiol to activate gene expression. They also assigned unique molecular barcodes to each gene, facilitating high-throughput sequencing experiments. This work not only showcases impressive experimental capabilities but also aids researchers in mapping the functions of yeast genes, a task that remains incomplete even for well-studied organisms.

Biomaterials, Made with Synthetic Biology

Biomaterials captivate me, particularly since I once heard Neri Oxman discuss the fascinating concept of “death masks” during my college years. A recent review delves into the realm of biomaterials—both living and non-living—and examines how they can be engineered using genetic circuits and synthetic biology tools. The authors explore the integration of living biosensors and therapeutic microbes within these materials. While the paper is not open access, the full text can be accessed through a provided link on Twitter.

Super Precise Genome Deletions

Prime editing serves as an advanced version of CRISPR-Cas9. By merging an inactive version of the Cas9 protein with an engineered reverse transcriptase enzyme, prime editors can insert or delete nucleotides precisely within the genome without causing double-strand breaks. In a new preprint, researchers led by Jay Shendure at the University of Washington developed a modified prime editing system called PRIME-Del. This system allows for the deletion of specific genomic regions (between 20 and 700 base pairs) with greater precision than current CRISPR/Cas9 methods. They also utilized PRIME-Del to insert short DNA fragments at various genome locations. Shendure highlighted on Twitter that this new technique is more accurate as it eliminates the need for double-strand breaks or non-homologous end joining, is less limited by PAM sequences, and can facilitate multiple deletions simultaneously.

Rapid-Fire Highlights

Here are a few more noteworthy studies and reviews worth your attention:

• My recent experience with the Impossible burger at Burger King sparked my interest in a new review comparing cell-based and plant-based meat production methods. (Nature Communications)
• Volvox, a type of light-sensitive green algae, can swim toward light by shutting off its flagella motor upon sensing illumination. A fascinating study combined a light projector with a microscope to capture and control their movement in a project named DOME (Dynamic Optical MicroEnvironment). (bioRxiv)
• The versatility of synthetic cells opens up exciting possibilities for custom-designed artificial cells. A recent review discusses how these cells can be engineered to detect various environmental molecules. (Trends in Biotechnology)
• A new review from Jennifer Doudna’s group examines how natural molecules interact with CRISPR-Cas systems, either enhancing or inhibiting their functionality. (Nature Chemical Biology)
• Researchers recently developed bacterial biofilms that can be manipulated with light, creating gradients of varying thickness and enabling light-responsive mineralization of hydroxyapatite. (Nature Chemical Biology)
• A Boston University study utilized synthetic transcription factor decoys to finely tune gene expression in E. coli, achieving a 16-fold increase in arginine production without mutations over time. (Nucleic Acids Research)
• A new protocol outlines the process for designing custom DNA nanopores, which can be integrated into cell membranes. (Nature Protocols)
• In another study, researchers introduced random genetic mutations in 47 yeast transcription factors to assess their impact on alcohol tolerance, potentially paving the way for yeast strains capable of producing higher alcohol content beers. (ACS Synthetic Biology)

Wishing you a fantastic week ahead! Until next Friday,

— Niko

Bonus Tweet: Interested in sequencing a genome while simultaneously determining its 3D structure? Check out this new method!