Heat-Protecting Gene in Corals & Human Cells Get an Upgrade...from Tardigrades (#15)

Plus: CRISPR, used on RNA, makes lots of off-target edits.

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Heating Breakthrough in Corals

As the earth heats, and the Great Barrier Reef melts away, scientists are scrambling for deeper insights into heat-tolerance in coral—specifically, which genes help corals cope with higher temperatures, and could gene editing be used to create heat-resistant variants?

A gene in fertilized coral eggs (Acropora millepora), called Heat Shock Transcription Factor 1 (HSF1), was mutated with CRISPR/Cas9. After one injection of the CRISPR/Cas9 components, 90% of the eggs carried mutations in that gene, causing drastic changes in how well the coral could handle heat later on. “The mutant larvae survived well at 27 °C but died rapidly at 34 °C,” the authors wrote. The higher temperature did not, however, cause any damage to normal, un-edited corals. The authors conclude, therefore, that HSF1 “plays an important protective role” in these stunning creatures. This study was published in PNAS. Link

Underwater corals. Credit: Pexels on Pixabay

Human Cells Upgraded with Tardigrade DNA

Astronauts and flight-attendants alike are bombarded with radiation. In one study, 1.2% of male flight attendants reported that they had melanoma, a rate nearly twice as high as the general population. Female flight attendants, similarly, have reported a skin cancer incidence that is four times higher than the general population. To protect these high-flying professionals, some scientists are turning to…tardigrades.

These little “sea bears” are so hardy that they can “survive up to 5kGy of ionizing radiation and also survive the vacuum of space,” according to the authors of a new preprint, posted on bioRxiv. For context, a typical abdominal x-ray is just 0.7 milligrays, or about 7 million times less radiation than tardigrades can withstand.

The researchers studied a damage suppressor protein from the tardigrades, called Dsup, that helps repair damage to DNA caused by ionizing radiation. They transplanted Dsup into human cells, grew the engineered cells in a dish, and found that the cells became more tolerant to apoptosis—or cell death—signals. The authors think that their “methods and tools provide evidence that the effects of the Dsup protein can be potentially utilized to mitigate such damage during spaceflight.” Link

A tardigrade swims by. Credit: GIF Maker/Giphy

Rapid Evolution Creates New TrpB Proteins

Creating proteins with new functions can, at least in the natural world, take hundreds or thousands of years of evolution. One protein begets another, through mutations, slowly unraveling a sea of new properties that help organisms adapt and survive in their environments.

But evolution can also be “jump-started” in the laboratory, and kicked into overdrive using relatively modern approaches called directed evolution. This technique—using evolution to design new proteins—earned Frances Arnold a share of the 2018 Nobel Prize in Chemistry.

In a new study, emanating from a collaboration between the labs of Chang Liu and Frances Arnold, a method for continuous, directed evolution, called OrthoRep, was used to create new variants of the tryptophan synthase β-subunit protein. This enzyme is important because it synthesizes L-tryptophan from indole and L-serine. Over 100 generations of the directed evolution experiment, the researchers created new TrpB enzymes that had higher activities, could use different indole analogs, or could work at different temperatures. This study was published in Nature Communications, and is open access. Link

Engineered Bacteria Respond to Inflammation Signals

Microbes that live in the human gut can be engineered to release medicines, or sense diseases. They are basically tiny, programmable doctors that could, one day, be used to treat all kinds of ailments.

In a new preprint, posted to bioRxiv, scientists at Caltech engineered E. coli Nissle cells with an AND logic gate that triggers a gene’s expression when two signals are present: tetrathionate (an inflammatory biomarker) and IPTG. The authors “report 4-6 fold induction with minimal leak when both signals are present.” These are interesting preliminary results, based on experiments done in flasks and tubes, and the next step will be to take these engineered cells, and see if they can actually sense inflammation inside of, say, a mouse gut. Link

Study Evaluates CRISPR-Cas Systems for RNA Editing

The gene-editing tool, CRISPR-Cas9, can be adapted to cut both DNA and RNA inside of living cells. Its utility for DNA-editing is well known, but RNA-editing applications have not been studied as carefully.

Catalytically inactive Cas9—that is, Cas9 that cannot cut DNA, but can still recognize and bind to a genetic target—can be fused to a protein called ADAR (adenosine deaminases acting on RNA) to make single-letter changes in RNA. These dCas9-ADAR proteins can switch A to I, for example, but it turns out that they have some issues.

The researchers of a new study from the Yeo lab at UC San Diego say that the “Cas-based ADAR strategies have distinct transcriptome-wide off-target edits”. They also performed experiments to figure out how to best design guide RNAs to target a specific nucleotide in an RNA strand. They found that, even without a spacer sequence, Cas9-ADARs could still edit RNA. This study was published in Cell Reports, and is open access. Link

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🧫 Rapid-Fire Highlights

More research & reviews worth your time

  • Stevia—the artificial sugar—can now be manufactured with microbes. Or, at least, a precursor to stevia, called ent-kaurenoic acid, can be. A new study reports that Synechoccous elongatus, a species of cyanobacteria, can biosynthesize 2.9 ± 0.01 mg per liter of the compound directly from carbon dioxide. ACS Synthetic Biology. Link

  • To create artificial cells that—like real cells—can actually process and respond to information, researchers will first need to find ways to create artificial cells that can respond to stimuli without requiring complex protein networks and metabolisms. In a new study, researchers found that, by reducing the copies of a gene from about 100,000 to 10, artificial cells can make decisions based on a small number of protein fluctuations. They say that their “results demonstrate information processing with low-power consumption inside artificial cells.” Nature Communications (Open Access). Link

  • A new, massive collection of bacterial and archaeal metagenomes has been reported. “This comprehensive catalog includes 52,515 metagenome-assembled genomes” that, together, expand “the known phylogenetic diversity of bacteria and archaea by 44%” This study is truly remarkable. Nature Biotechnology. Link

  • Even the most simple genetic circuits—like those made of just two proteins—can be a complicated mess. A new study shows that mathematical models may fail to accurately predict how even these basic genetic circuits will behave in cells, and that prescient predictions “requires mapping the dose responses of each circuit component along the dimensions of both its expression level and its inducer concentration.” ACS Synthetic Biology. Link

  • Inside of cells, everything is in a constant state of competition. Molecules and proteins jostle for attention inside of cells with finite resources. A new study reports a feedforward controller—that uses CasE, a type of CRISPR protein—to decouple resource-limited genetic circuits. Nature Communications (Open Access). Link

  • Liquid-like droplets of proteins, formed inside of cells, are called protein condensates. A preprint reports a new technique to create synthetic protein condensates inside of mammalian cells. The synthetic protein condensates can release proteins when triggered by a small molecule, or light. bioRxiv (Open Access). Link

  • “Microrobots” are in vogue; swimming bacterial drug delivery systems, engineered red blood cells, and even teeny electronics have been proposed as futuristic medical treatment options. A new review breaks down the science of these microrobots, specifically in the context of cancer therapies. Nature Communications (Open Access). Link

  • Prime editors can swap bases, delete nucleotides, and insert DNA into the genomes of cells. But they are still, largely, limited by the PAM sequence of S. pyogenes Cas9. A new study reports several prime editing mutants that are more permissive in their DNA targeting; they can recognize, and cut, near different PAM sites. bioRxiv (Open Access). Link

  • The European Union demands that GMO foods be both labeled and traceable (among other things). A new review analyzes the technological risks of GMOs, frames them in a historical perspective, and compares GMO regulation in Europe to that in the U.S. Frontiers in Bioengineering and Biotechnology (Open Access). Link

  • Pichia pastoris, a type of yeast, can feed on methanol. That makes it an attractive platform for metabolic engineers looking to make drugs and chemicals from a single-carbon compound. dCas9 fused to an sgRNA scaffold and activation domain was used to selectively upregulate gene expression in these little critters. ACS Synthetic Biology (Open Access). Link

  • CRISPR/Cas9 was used to correct a specific mutation, called p.F508del, in the cystic fibrosis transmembrane conductance regulator gene, or CFTR. The mutation was corrected in two types of human cells, including pluripotent stem cells derived from cystic fibrosis patients. PLOS ONE (Open Access). Link

📰 #SynBio in the News

  • Retrons are CRISPR’s ugly cousin. But new breakthroughs in retron research could expand their usefulness to synthetic biologists. Science. Link

  • Gene-editing could create “heat-resistant” cows, helping farmers adapt to one of the many challenges that will emanate from a warming planet. Future Human. Link

  • Learn about how biotechnology and art are merging at Philadelphia’s Science Center; a new piece from Kathryn Hamilton. Bioeconomy.xyz. Link

  • Microbes could be repurposed as “space rock” harvesters. That’s a bold speculation, but is based on new experiments that were conducted aboard the International Space Station and reported in Nature Communications this week. MIT Technology Review. Link

  • Ginseng, grown in the Appalachian mountains, is in danger. Can farmers save the over-harvested plant? I love this story, even though it’s not #SynBio. Undark / Popular Science. Link

  • A long read on gene drives, featuring Imperial College’s Alekos Simoni, explains how they could be used to fight malaria. Labiotech.eu. Link

  • And, of course, the biggest news this week: Pfizer’s COVID-19 vaccine is 90% effective. The company says that, by year end, they plan to manufacture 15 to 20 million doses. New York Times. Link

🐦 Tweet of the Week

New research from Chang Liu’s group at UC Irvine leveraged “hypermutated” yeast to create high-affinity antibodies against SARS-CoV-2. Read his explainer thread, and check out the preprint, on Twitter 👇

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