An unusual blue jellyfish opens up doors to new fluorescent proteins


A team lead by the University of California San Diego has unveiled the unique properties of fluorescent proteins in an unusual Australian blue jellyfish. At the ESRF, they discovered a novel chromophore, the protein component that absorbs and emits light.

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Fluorescent proteins are a method widely used by the scientific community to image live cells. This has proved useful to track the development of nerve cells in the brain or to monitor how cancer cells spread. These proteins come mostly from marine invertebrates. The first one ever sequenced was the Green Fluorescent Protein (GFP), from the jellyfish Aequorea victoria in 1992, and revolutionized biology when it was turned into a tool to be used in mammalian cells. The Nobel Prize in Chemistry was awarded to the ‘fathers’ of this protein in 2008.

Fast forward several years, and a team of scientists are on an expedition to Heron Island, a research station on the Great Barrier Reef in Australia. “We were set to collect plankton, invertebrates floating in the water. We do that by free diving or snorkeling. By chance, we caught a jellyfish that looked really interesting: it was navy blue, which is a very uncommon colour. So we decided to keep its RNA, preserve it and get it sequenced when we would be back home”, explains Nathan Shaner, leader of the study, about his first encounter with the jellyfish. Shaner, whose mentor was the Nobel Prize laureate Roger Tsien, is a professor at the University of California San Diego.

While in Australia, the researchers emailed a colleague in Monterey Bay Aquarium to try to find out more about the species. It turns out that it is a very similar species to Aequorea victoria.  So once back home, the scientists looked for sequences that looked like the GFP from Aequorea victoria, but surprisingly, they found other fluorescent, very unusual proteins.

“So we went back to Aequorea victoria, which we got from the Birch Aquarium, and compared both. It turns out that after GFP was discovered, no one has looked into the jellyfish again in all these years. We discovered a similar set of fluorescent proteins in both specimens, but with notable differences”, explains Shaner.

The Australian jellyfish’s proteins include chromoproteins that are bluer and a fluorescent protein that is much brighter than the Aequorea victoria’s GFP. The Aequorea victoria chromoproteins also need light to turn into different colours, which is not the case for the Australian proteins.

The scientists discovered five new fluorescent proteins in the Australian jellyfish and came to the ESRF to solve the structure of the two most interesting ones: an extremely bright green protein and the protein that absorbed the most red light. “It was a massive effort. Antoine Royant, one of the world experts in solving fluorescent protein structures, led the team to crystallise the proteins first and then study them using X-ray crystallography”, says Shaner.

The results shed light into the optical properties of the proteins and found a novel chromophore, which is the part of the protein that absorbs and emits light. Antoine Royant, scientist at the ESRF and the Institut de Biologie Structurale, says: “Together with my students and postdocs, we have been solving the structures of many fluorescent proteins since 2005, but I keep being amazed by the variety of chemical reactions that can occur around, or on the chromophore. When we first saw the electron density of this novel chromophore, we could not believe it, and we had to resort to additional biochemical experiments in San Diego and theoretical calculations in Paris to be perfectly convinced of its structure”.

The chromophore in the blue protein is chemically different from any other chromophore found before. It presents a mechanism whereby it absorbs a lot of green and red light rather than absorbing blue light. On the other hand, the chromophore in the green protein exhibits a very different chemical environment, which accounts for why it is so bright and has such a narrow spectrum.

 A crucial aspect of the Australian protein is that it has a very narrow peak in its emission, so there is less of the light in other areas of the spectrum. The narrowness of the peak means that researchers could image more events in a cell at the same time using additional fluorescent colours.

The team is now working hard to turn this wild-type protein into a new tool and optimise it for the people in the research community to use.

“The great thing about this paper is that we went from field biology, collecting animals in the ocean, all the way to solving the structures, finding new chemistry in the proteins and understanding them at that level. It was definitely a full-spectrum study”, concludes Shaner.


Lambert, G.G., PLOS BIOLOGY, November 2020.

Text and video Montserrat Capellas Espuny. Pictures used in the video by Nathan Shaner



Top image: Aequorea Australis, the jellyfish with 5 fluorescent proteins. Credits: N. Shaner