Data Erasure in DNA: A Good Problem to Have

DNA is emerging as a leading option for data storage, with the astonishing capability of holding 256 petabytes of information in just one gram. However, its excessive stability presents challenges. For future "nucleic acid hard drives," researchers must devise methods to selectively erase data.

A promising technique detailed in Nature Communications proposes a solution for potentially wiping data from DNA by 2087 (if humanity persists that long). In this method, DNA sequences with a “True” barcode and one or more “False” barcodes are mixed. Researchers then introduce “truth markers” that specifically attach to the “True” sequences. By heating the mixture to 95 degrees Celsius, the truth markers detach, leading to a loss of information from the “True” segments. This straightforward technique shows great potential.

The study demonstrated that “eight distinct bitmap images could be reliably stored and retrieved after being kept at 25 °C for 65 days, achieving over 99% accuracy. However, heating it to 95 °C for five minutes permanently deletes the data.”

Enzymatic Pathways Constructed on a Virus

An enzymatic pathway has been developed on a Tobacco mosaic virus. Scientists from Hong Kong connected three terpene biosynthetic enzymes to the virus's outer surface using peptide linkers, then cultivated them in E. coli cells. The aim was to investigate how the proximity of enzymes affects the production of a specific molecule, amorpha-4,11-diene.

Given that the Tobacco mosaic virus is 300nm long, metabolic engineers might utilize it as a scaffold for assembling various intricate enzymatic pathways. This work was published in Bioconjugate Chemistry.

Deep Learning for RNA Switch Design

Two studies featured in Nature Communications applied deep learning techniques to create RNA “toehold switches.” These synthetic RNA sequences can be toggled ON and OFF. In their OFF state, the toehold switches form a hairpin loop, rendering them unreadable by ribosomes, thus halting protein production. However, the introduction of an RNA “trigger” can activate the switch, allowing translation to occur.

Toehold switches are particularly advantageous because multiple switches can coexist within a single cell, and individual triggers can be designed for each. This allows for precise control over various genes in synthetic biology applications. Yet, designing these switches is complex, as even minor modifications can influence their effectiveness.

In the first study led by Nicolaas M. Angenent-Mari, researchers synthesized and tested over 90,000 toehold switches through innovative experiments to evaluate each switch's activity. The data collected was then input into a deep learning model. The results were promising: “[Deep Neural Networks] trained on nucleotide sequences significantly outperformed (R2 = 0.43–0.70) traditional thermodynamic and kinetic models (R2 = 0.04–0.15).”

The second study, led by Jacqueline Valeri, introduced two deep learning architectures—STORM and NuSpeak—to enhance RNA toehold switch performance. Both studies are publicly accessible and signify a transformative shift in the speed at which synthetic biologists can design and engineer biological molecules.

Engineering Rice with C4 Photosynthesis

Most plants are classified as C3 plants, which close their stomata in hot or dry conditions, causing a buildup of oxygen and reduced photosynthetic efficiency. Conversely, C4 plants have evolved mechanisms to prevent oxygen accumulation. In C4 plants, carbon dioxide fixation occurs in mesophyll cells, while the Calvin cycle takes place in bundle-sheath cells, allowing for improved photosynthesis efficiency.

A recent study published in Plant Biotechnology Journal introduced five genes into a specific rice strain, resulting in a modest 2% increase in photosynthetic flux. While the results are preliminary, they hold promise for enhancing rice yields, which are crucial for over half of the world's population.

Characterizing Genetic Circuits

Biological circuits within cells are composed of numerous genetic components. Even slight alterations to elements like promoters or ribosome binding sites can significantly affect circuit performance. A new study meticulously examined all 54 components in a circuit, parameterized them, and developed a mathematical model to predict circuit behavior, dynamics, and robustness. They also estimated the cellular power (RNAP and ribosome usage) needed to sustain a circuit state. This research was published in Nature Communications and is freely accessible.

Rapid-Fire Highlights

More research and reviews worth your time:

• Gut microbes can be selectively targeted using phages carrying dCas9, demonstrating effective gene repression within a mouse gut. Nature Communications (Open Access). Link
• The need for DNA polymerases to replicate expanded genomes is explored in an insightful review. The Journal of Biological Chemistry (Open Access). Link
• A preprint from the Leonard lab outlines a model-driven method for constructing genetic circuits in mammalian cells without trial-and-error. bioRxiv (Open Access). Link
• Researchers discovered the ZIM3 KRAB domain as the most potent gene repressor after screening 57 protein domains fused to dCas9. Nature Methods. Link
• CRISPR technology was used to delete an allele of the CCR2 gene in poplar plants, resulting in 10% less lignin, facilitating easier sugar extraction. Nature Communications (Open Access). Link
• A preprint simulated eight minimal gene sets from Mycoplasma genitalium, aiming to identify viable minimal cells. bioRxiv (Open Access). Link
• Research on JCVI-syn3.0 revealed that adding just 19 genes can eliminate significant morphological variations. bioRxiv (Open Access). Link
• Scientists in India discovered “iron-sensing bacterial riboswitches” that respond to reduced iron. Nature Chemical Biology. Link
• A new study utilized proteases to create genetic circuits, including an analog to digital converter. Nature Communications (Open Access). Link
• A review covers genome editing systems across various yeast species. Current Opinion in Biotechnology (Open Access). Link
• A preprint offers insights into analyzing trans-acting factors alongside gene expression in MPRAs. bioRxiv (Open Access). Link
• A new CRISPR/Cas9 and RNAi screening database, CRISP-view, curates datasets from 167 relevant studies. Nucleic Acids Research (Open Access). Link
• The Rios lab published a review on multiplexed CRISPR methods for yeast. Frontiers in Bioengineering and Biotechnology. Link
• A study created engineered cells that respond to fluoride through fluoride-responsive riboswitches. Nature Communications (Open Access). Link
• CRISPRoff is a new method that degrades sgRNAs in living cells using light, causing CRISPR activity to cease. Nature Communications (Open Access). Link

A Correction

In last week’s newsletter, I discussed a study on engineered E. coli that can thrive on carbon dioxide and formate. I overlooked earlier research by Arren Bar-Even's lab, which also reported similar findings in February of this year, published in Nature Chemical Biology. I apologize for the omission.

#SynBio in the News

• Doudna and Charpentier received the Nobel Prize in Chemistry this week, with coverage from various outlets, including The New York Times and Nature. I particularly appreciated Quanta’s take on the announcement. Link
• UC-Berkeley scientists, including Doudna, announced Scribe Therapeutics, aiming to develop a novel CRISPR platform for treating genetic disorders. Link
• A thought-provoking op-ed in bioeconomy.xyz questions whether life scientists should reassess their career tracking methods. Link
• Medieval cesspits reveal fascinating ancient microbiomes, as discussed by Ars Technica. Link
• Enzymatic DNA synthesis companies were featured in a Nature Biotechnology article. Link
• Kevin Davies has released a new book titled “Editing Humanity: The CRISPR Revolution and the New Era of Genome Editing.” GenEng News conducted an interview with him. Link
• Motif Foodworks is set to launch its first synthetic biology-based food product. Link
• COVID-19 vaccines cultivated in plants? Leslie Nemo reports for Future Human. Link
• The Howard Hughes Medical Institute will mandate that all scientists make their papers freely available online starting in 2022. Reported in Science. Link
• Phosphine detection on Venus raises questions about potential life, though with many caveats, as noted by Caleb Scharf in Scientific American. Link

Tweet of the Week

This week’s standout tweet is the announcement of the 2020 Nobel Prize in Chemistry. The recognition for Doudna and Charpentier marks a significant milestone for synthetic biology, following Frances Arnold’s Nobel win in 2018. Check it out!

Thank you for reading This Week in Synthetic Biology, part of Bioeconomy.XYZ. If you find this newsletter valuable, please share it with a friend. You can reach me with tips and feedback via Twitter direct message at @NikoMcCarty.