Osamu Shimomura – EMBL Communications

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Osamu Shimomura

Organic chemist who paved the way for modern-day fluorescent microscopy

Many organisms derive their energy from sunlight – and some produce light themselves to communicate with, attract, or repel other organisms. Osamu Shimomura spent most of his life studying these organisms and their proteins, trying to understand how they generate light. The start of Osamu’s scientific career in postwar Japan was anything but easy, but dedication, hard work, and a few lucky coincidences opened doors and enabled Osamu to embark on a successful research career. His work led Osamu to discover Green Fluorescent Protein – the prototype of fluorescent proteins that has become an indispensable tool for biologists to study the functions of proteins, cells, and organisms.

Osamu Shimomura. Image Credit: Rayne Zaayman-Gallant/EMBL

Quick facts

27 August 1928 – 19 October 2018

Japanese pharmacist and organic chemist; Nobel Prize in Chemistry (2008)

Important discoveries: Studied the light-emitting proteins from various organisms; discovered Green Fluorescent Protein (GFP), which has become an indispensable tool in microscopy and cell biology research

Osamu Shimomura was born and grew up in a city near Kyoto in Japan. His childhood was marked with frequent moves between homes, including to the Chinese province of Manchuria for a while, as his father was a captain in the Japanese army. Most of the time, Osamu lived with his mother and siblings, and for about a year, when both his parents were abroad, Osamu was raised by his grandmother.

In seventh grade, Osamu contracted tuberculosis, and despite trying hard to keep up with schoolwork, his grades were poor. Osamu recovered, but shortly afterwards his school education was interrupted once more by the events of World War 2. Classes came to a complete halt at the beginning of tenth grade, and the students were sent to work in factories to support the economy. When one of these factories was attacked by airplanes, Osamu only survived because he had hidden in the fields, rather than in an underground shelter like many of his co-workers.

When the war was over, Osamu wanted to enter college, but due to his poor school education, the first three colleges rejected him. He then applied to Nagasaki Pharmacy College, and to his surprise he got accepted. Even though Osamu didn’t intend to become a pharmacist, he took up studies in Nagasaki under dire post-war conditions. There was little food and life was characterised by shortages in everyday goods and laboratory equipment.

Despite the difficult situation, Osamu did very well in college and developed an interest in chemical experiments. His first mentor, Professor Shungo Yasunaga, even allowed him to take some materials from the lab to his home to continue his experiments, and in 1951, Osamu graduated at the top of his class. The professor offered him an assistant position in an analytical chemistry laboratory, which Osamu gladly accepted. He worked for Yasunaga for the next four years.

One day, Yasunaga took Osamu on a visit to Nagoya University to introduce his young colleague to the well-known molecular biologist, Professor Fujio Egami. Unfortunately, Egami wasn’t in his office on that day, so Yasunaga and Osamu stopped by to say hello to Professor Yoshimasa Hirata, an organic chemist. The scientists chatted for a couple of minutes. When Osamu and Yasunaga were about to leave, Hirata surprisingly offered Osamu to join his organic chemistry lab at any time – and Osamu accepted the offer.

Illustration of elderly male scientist, bright green jellyfish in the background.
Portrait of Japanese organic chemist Osamu Shimomura, who discovered Green Fluorescent Protein while studying Aequorea jellyfish. Image Credit: Rayne Zaayman-Gallant/EMBL

In spring 1955, Osamu began to work in Hirata’s lab as a research student. He was given the task to study Cypridina, a small crustacean that’s commonly found along the Japanese coast. Cypridina uses an organic molecule called luciferin and a protein called luciferase to convert chemical energy into visible light in a process called bioluminescence. Other scientists had tried to study luciferin and understand its chemistry for decades, but their efforts had mostly failed – luciferin is highly unstable and decomposes quickly when exposed to air. Osamu’s task was a difficult project with the potential to fail badly, and he accepted it only because he was not studying towards a degree. 

But things turned out favourably. With dedication and hard work, and to Osamu’s and his professor’s surprise, it took Osamu only about ten months to extract and purify luciferin in the form of tiny crystals – a requirement to study its chemical structure. Osamu continued to work at Nagoya University for a few years, but in 1959, he received an invitation from the American researcher Frank Johnson to join his lab at Princeton University. When Osamu told Hirata about his plans, the professor awarded Osamu a Ph.D. degree in organic chemistry, in recognition of Osamu’s successful work on luciferin.

In September 1960, Osamu moved to the United States to join Frank Johnson’s research group, where he continued to work on bioluminescent proteins. The research project that Frank asked Osamu to do involved the jellyfish Aequorea, which is capable of glowing in the dark. Initial experiments on freeze-dried light organs from the jellyfish failed – the scientists apparently needed fresh specimens to study their bioluminescence. For the first couple of months at Princeton, Osamu therefore studied luciferase, which he could obtain in huge quantities from dried Cypridina samples that were available in the lab.

In summer 1961, however, the Aequorea project moved forward. Osamu and his colleagues visited Friday Harbor in the north-western state of Washington to collect Aequorea, which were highly abundant at the coast. The scientists stayed for three months until they had collected enough jellyfish to extract the protein that made the animals produce light. Back in the lab, the team managed to obtain a small amount of the pure protein, which they named aequorin. But surprisingly, the researchers also found a second protein, which would send out bright green light when put under a blue light source. They named this protein Green Fluorescent Protein – or GFP in short. Osamu and his colleagues didn’t expect that GFP, which was just a curiosity of nature at that time, would later transform experimental biology.

Over the next 40 years, Osamu continued to study light-producing proteins in laboratories in Japan, at Princeton, and later at the Marine Biological Laboratory in Woods Hole, Massachusetts. He continued his work on luciferin, aequorin and GFP, and studied the peculiarities of a whole range of organisms capable of producing light. His zoo of study objects grew from year to year and came to include various worms, freshwater limpets, krill, firefly squids, millipedes, brittle stars, and several types of luminous bacteria and mushrooms.

To understand the structure of the aequorin protein, it took Osamu and his colleagues about 12 years of work and regular trips to Friday Harbor each summer to collect jellyfish. In 1972, they managed to solve part of the structure of the protein, and six years later, they understood the chemical reactions that led to the production of light. In 1979, Osamu described the molecular structure of GFP that is responsible for its green fluorescence.

With a better understanding of the GFP protein came the idea to use it as a tool in experiments. In the 1990s, American biologist Martin Chalfie managed to make bacteria and nematode worms produce functional GFP, and Roger Tsien modified GFP’s chemical composition and obtained various related proteins emitting light of different colours.

Since then, scientists have found ways to make cells of almost any type produce these fluorescent proteins – from bacteria and yeast cells, via flies, fish and mice, to human cells growing in a petri dish. By attaching GFP or one of its colourful protein ‘colleagues’ to other proteins, researchers can observe the location of these proteins inside a cell, or find cells they’re interested in within a tissue sample or an entire organism under the microscope. GFP can be used to study where and when proteins are produced, how they move through cells, where and how they do their job, and when they get recycled. Over time, biologists came up with a plethora of ideas on how to use GFP as a tool in their experiments.

The foundations for these applications, however, were laid by Osamu, Martin, and Roger. In recognition of their accomplishments, the three scientists were awarded the shared 2008 Nobel Prize in Chemistry. The other proteins Osamu had studied found applications in physiological, molecular and cell biological research as well. Luciferase and luciferin have been applied in molecular biology experiments to measure the activity of genes. Aequorin can be used as a biological calcium sensor to study how muscles function, and it’s also used to investigate other processes in cells that involve calcium ions.