Jellyfish Reveal More Glowing Secrets & Bacteria Make Purple Sea Snail Dye
By: Niko Mccarty
Tags: Newsletter, CRISPR, News, Science, Future

NEWSLETTER

Jellyfish Reveal More Glowing Secrets & Bacteria Make Purple Sea Snail Dye

This Week in Synthetic Biology (Issue #14)

Receive this newsletter every Friday morning! Sign up here: https://synbio.substack.com/

Tell me about your research on Twitter.

The Crystal Jelly Unveils Its Brightest Protein Yet

Aequorea victoria, the crystal jelly, hovers in the waters off the coast of California. Decades ago, Osamu Shimomura noticed that these jellies emit a faint, green light. So he took pieces from one of them, did some experiments, and found the protein responsible for the glow. That protein — GFP — is now used in thousands of labs to light up the insides of microscopic cells. Shimomura shared the 2008 Nobel Prize for that work, along with Martin Chalfie and Roger Tsien, who died in 2016.

Now, it looks like the crystal jelly hasn’t given up all of its secrets just yet.

In a new study, nine previously unstudied proteins, also from Aequorea victoria and a related species, were reported. Several of the new fluorescent proteins have quirky characteristics, too. One of them is “the brightest GFP homolog yet characterized”, while another protein can respond to both UV and blue light. The scientists even found a couple of purple and blue-pigmented chromoproteins. The findings are further evidence that, in the darkness of the oceans, scores of mysteries remain to be discovered. This work was published Nov. 2 in the open-access journal PLoS Biology. Link

Will DNA Replace Grocery Store Barcodes?

A standard barcode — think grocery store rectangle, with black-and-white lines — contains 11 digits. Mixing up those digits in every possible way gives about 100 billion possible combinations. That’s a lot, but it’s not nearly as many combinations as what a barcode made from DNA could provide.

A new study, published in Nature Communications, reports a molecular, DNA tagging system that could become the future of barcodes. The DNA was dehydrated, which made it more stable, and the sequences were read out in just a few seconds with an Oxford Nanopore MinION, a small, portable DNA sequencer. To facilitate that speed, the authors came up with some clever ways to avoid complex, computational analysis of the DNA signals; they were able to read the barcodes directly from the raw sequence data. This study was published Nov. 3 and is open access. Link

Bacteria Produce Tyrian Purple Dye (From Sea Snails!)

As early as 1570 BC, the Phoenicians were dying fabrics with Tyrian purple. To make the dye required a process so intensive as to be nonsensical; as many as 250,000 sea snails (Bolinus brandaris) had to be smashed into goop to make just one ounce of dye. It was a color reserved for royalty, and literally worth more than its weight in gold.

Thank goodness, no more snails need to be smooshed to make Tyrian purple dye. Engineered E. coli bacteria can now make the dye’s predominant chemical, called 6,6'-dibromoindigo. To achieve this, scientists from Seoul National University added several genes to the bacteria; a tryptophan 6-halogenase gene, a tryptophanase gene and a flavin-containing monooxygenase. That’s a mouth garbling sentence, but I promise the result is easier to understand: the cells were able to produce 315 mg of 6,6'-dibromoindigo per liter in flasks, using tryptophan — an animo acid — as the chemical precursor. This work was published Nov. 2 in Nature Chemical Biology. Link

79 Different Cas9 Proteins Were Tested. Some Are Wicked Cool

Cas9 is maybe the most famous protein on earth. It’s like, the Kim Kardashian of the protein world. If there was a magazine for proteins, Cas9 would be on its cover. Oh wait, that already happened.

There’s a lot of different Cas9 proteins, but not all of them have been characterized. In a new study, scientists identified, and tested, 79 different Cas9 orthologs — proteins taken from different species, but that have the same function — and figured out how they recognize and cut DNA. Intriguingly, some of the Cas9 proteins only worked at specific temperatures; Cme2 Cas9, for example, “was only robustly active from ~30 °C to 55 °C suggesting the possibility of temperature-controlled DNA search and modification.” This study was published Nov. 2 in Nature Communications, and is open access. Link

CRISPR Shuts Down Fertilized Eggs

I didn’t know about the birds and the bees until my parents sat me down and told me. But if you’re wondering, a typical pregnancy starts like this: a fertilized egg latches on to the endometrium in the uterus. That activates a flood of genes to turn “on”, including one called leukemia inhibitory factor, or LIF. A new study has figured out a way to cut off fertility — with CRISPR — by targeting LIF and switching it “off”. The reason this is cool is because, well, the CRISPR-Cas9 system is photoactivatable, meaning it can be switched on with an LED.

The scientists, from Keio University in Tokyo, think that their work could prove useful in basic science research that probes the molecular signals underpinning this process. The study was published Nov. 2 in the journal PNAS, and is open access. Link