Automated DNA Cloning Revolution

Picture this: it's midnight in the laboratory. Your colleagues have all left, and you're left alone, anxiously wondering if a security guard might interrupt your work. If you've ever found yourself in this predicament, it might be due to your struggles with a particularly challenging DNA cloning task.

Fortunately, the future holds promise. Automation is advancing, with robots set to take over entire experiments, including the creation and cloning of custom DNA sequences. However, a crucial part of the cloning process—using electricity to help cells absorb DNA—has posed challenges for automation.

A recent study published on November 24 in ACS Synthetic Biology introduces a fully automated DNA cloning method that utilizes "natural transformation" instead of electroporation. Researchers from Sang Yup Lee's lab at the Korea Advanced Institute of Science and Technology demonstrated that the bacterium Acinetobacter baylyi can naturally uptake DNA without requiring specialized equipment. While it was known that A. baylyi is "naturally competent," this marks a significant first in fully automating the DNA cloning process.

The research team simply added DNA sequences to a liquid containing A. baylyi, which eagerly absorbed the DNA and began replicating it, generating tens, then hundreds, and eventually thousands of copies.

The authors noted, "No DNA purification, competence induction, or special equipment is required. Up to 10,000 colonies were obtained per microgram of DNA, with minimal false positive colonies." They successfully cloned 21 biosynthetic gene clusters ranging from 1.5 to 19 kb, demonstrating consistency when executed by an Opentrons robot. Check out the paper! [Link]

Bacteria Engineered for Copper Remediation

Researchers from the University of York and Umeå University in Sweden have engineered E. coli bacteria to accumulate significant amounts of copper.

To achieve this, the team combined seven different protein segments—each believed to bind copper ions—with Maltose Binding Protein (MBP). When expressed within bacterial cells, these protein chimeras "conferred tolerance to high concentrations of copper sulfate," according to the authors. Remarkably, some bacteria exhibited tolerance to copper levels "160 times higher than the recognized EC50 toxic levels in soils."

Additionally, the researchers analyzed data and concluded that these copper-binding proteins might have the potential to bind other metals. They propose that these bacteria could be engineered for the removal of other hazardous heavy metals or for bio-mining rare metals. Let’s mine some asteroids with engineered space bacteria!

This work was published in Scientific Reports and is open access. [Link]

Insights from Gene Knockdown on Metabolic Healing

When a bacterium is introduced to a new environment—such as one rich in sugar or populated by different competitors—it quickly adapts its metabolism. Notably, a 2016 study by Schmidt et al. in Nature Biotechnology found that the total mass of a bacterium's enzymes could double in response to environmental changes.

But what happens when just one gene, responsible for a single enzyme, is silenced or knocked down? How does the intricate metabolism of the cell adjust to this deficiency?

It turns out that cells reorganize their resources in fascinating ways to "heal" a metabolic deficiency. A study published on November 24 in Cell Systems employed CRISPR interference (CRISPRi) to systematically repress individual genes in E. coli cells. Researchers utilized an inducible version of CRISPRi to control enzyme levels and observe the metabolic responses.

The team repressed 1,515 metabolic genes, generating 4–6 sgRNAs for each gene, culminating in a total of 7,177 unique E. coli strains. They then induced the CRISPRi system and measured the delay between induction and the emergence of fitness defects.

Thirty strains were examined closely, revealing intriguing examples of how metabolism adjusts to compensate for a deficient enzyme. "Our results underscore the pivotal role of regulatory metabolites in maintaining robustness against fluctuating enzyme concentrations in cells," the authors concluded.

For a more accessible overview of this study, check out the press release. This study is open access. [Link]

Laboratory-Evolved Bacteria Investigate Antibacterial Resistance

The rise of drug-resistant bacteria is a significant concern, prompting researchers to develop new antibiotics. To enhance antibacterial compounds, it’s essential to understand how resistance mechanisms evolve.

Published on November 24 in Nature Communications, a team from RIKEN and the University of Tokyo implemented an automated robotic system to evolve bacteria over more than 250 generations while exposing them to 95 different antibacterial agents. Essentially, they placed the cells into an accelerated evolutionary process.

By analyzing the evolved strains and their gene expression profiles, the researchers utilized a machine learning algorithm to identify specific gene expression "signatures" associated with drug resistance in these microbes. Read the press release on this open-access study. [Link]

Precise DNA Insertion Using CRISPRi

A novel type of CRISPR-Cas system derived from Vibrio cholerae has enabled researchers to insert large DNA segments, up to 10,000 base pairs, at precise locations within bacterial genomes with purported 100% efficiency.

The team from Columbia University named their approach INTEGRATE (insertion of transposable elements by guide RNA–assisted targeting). After successfully inserting DNA at a single genomic site, they expanded their efforts to insert DNA at three different genome locations simultaneously by expressing multiple guide RNAs. This method was published in Nature Biotechnology. [Link]

Rapid-Fire Highlights

SynBio in the News

• Ginkgo Bioworks has secured a $1.1 billion loan from the U.S. International Development Finance Corp to expand its COVID-19 vaccine manufacturing efforts. Reuters. [Link]
• Researchers are editing the CCR5 gene in monkeys as a potential HIV treatment. The monkeys have not yet been exposed to the virus. This is the same gene altered by He Jiankui during the CRISPR baby controversy. Future Human. [Link]
• Biomanufacturing firm Genomatica has partnered with Aquafil, a nylon production company, to establish a new demonstration-scale facility. Could pantyhose made from microbes be on the horizon? Tech Crunch. [Link]
• Interim data suggests that the new Oxford/AstraZeneca vaccine has an effectiveness of up to 90%, although a dosing mix-up has caused confusion among scientists and the public. MIT Technology Review and Science.
• The Institute for Protein Design has shown that "designer proteins" can bind to and deactivate a portion of the SARS-CoV-2 virus responsible for COVID-19. Katherine J. Wu featured their work during the pandemic in The New York Times. [Link]
• Japanese biomaterials company Spiber, in collaboration with sportswear brand Goldwin, is set to launch a sweater made from synthetic, protein-based materials. Forbes. [Link]
• A number of deserving synthetic biologists have been named as 2020 AAAS Fellows. Check out the full list in Science. [Link]
• (Not SynBio) Over 500 years, Leonardo da Vinci’s sketches have developed their own unique microbial collection. Wired. [Link]
• (Not SynBio) If you enjoy Impossible burgers, be cautious regarding your bone health! A study indicates that "meat-free diets are linked with a higher risk of bone fractures." New Scientist. [Link]

Tweet of the Week

Cell Reports has published a special issue featuring research at the intersection of space travel and biology. Check it out!

One paper that particularly piqued my interest is a longitudinal study on aging based on 520 days of simulated space travel.

Thank you for reading This Week in Synthetic Biology, a part of Bioeconomy.XYZ. If you appreciate this newsletter, please share it with a friend or colleague.

Feel free to reach out to me on Twitter at @NikoMcCarty or via email with any tips or feedback.