Akemi Shimomura, Scientist and Falmouth Resident, Dies at 86

Akemi (Okubo) Shimomura
Akemi (Okubo) Shimomura. Photo by Tom Kleindinst.

FALMOUTH, Mass. - With sadness, the Marine Biological Laboratory (MBL) notes the passing of Akemi (Okubo) Shimomura, aged 86, on May 11, 2022, at Cape Cod Hospital. The MBL flag will be lowered in her memory.

A biochemist, Mrs. Shimomura worked at the MBL from 1982 to 2001 as research assistant to her late husband, MBL Distinguished Scientist Osamu Shimomura, co-recipient of the 2008 Nobel Prize in Chemistry for the discovery of green fluorescent protein (GFP). Akemi participated in her husband’s research endeavors for more than four decades while raising their children and maintaining the family’s home, first in Princeton, N.J., and since 1981 in Falmouth.

She is survived by her son, Tsutomu and his wife, Kamila (Součková) of Incline Village, NV, and Zürich, Switzerland; her daughter, Sachi and husband John Brinegar of Richmond, VA; her granddaughters, Emi and Mika; and five siblings in Japan: Yoshimi Yamane, Yasusuke Okubo, Tadashi Okubo, Akihiro Okubo, and Takeshi Okubo.

The family funeral will take place in Japan, but a private preliminary service will be held on Tuesday, May 24 at 10 AM, and friends of Akemi are invited to keep her in their thoughts at this time.

Akemi Okubo was born on February 5, 1936 in Nagasaki, Japan, the daughter of Tomowo and Itsuko Okubo. When she was nine years old, on August 9, 1945, the U.S. military dropped an atomic bomb on Nagasaki, incinerating the city. Akemi was 1.5 miles from the center of the blast at a friend’s home; she and another child spent hours that afternoon seeking shelter, traversing the city’s ruins. Her oldest brother, Akira, died in the bombing. Akemi firmly opposed atomic weapon use all her life, based on her early memories.

After the war, with limited educational options available, Akemi enrolled in and graduated from the Nagasaki College of Pharmacy, where she studied chemistry. She married Osamu Shimomura, also of Nagasaki, on August 4, 1960, in Tokyo. Although their marriage was arranged by relatives in the traditional manner, they were acquainted: Shimomura had also graduated from Nagasaki College of Pharmacy and had trained Akemi during a short course. They would remain married for 58 years, until Osamu’s passing in 2018.

Shortly after their wedding, Osamu left Japan to accept a research position in the laboratory of Frank H. Johnson at Princeton University, a leading figure in the study of bioluminescence, the emission of light by living organisms. After receiving her visa, Akemi joined Osamu in Princeton in January 1961.

That summer, the Shimomuras, the Johnsons, and a research assistant drove across the United States to Friday Harbor Laboratories, University of Washington, to pursue research on the bioluminescent jellyfish Aequorea, which was abundant at Friday Harbor. Osamu wanted to define the biochemical reactions that caused the organism to bioluminesce. The team, including Akemi, hand-netted more than 10,000 jellyfish specimens that summer, cut off the luminescent edge of their umbrellas, squeezed out the extract, and brought it back to Princeton for study. In February 1962, Shimomura purified a nearly pure luminescent substance from the extract, a protein he named aequorin. He also purified a fluorescent protein from the extract, now called green fluorescent protein.

Akemi Shimomura
Akemi Shimomura at a ceremony marking Osamu Shimomura's receipt of the Order of Culture from the Emperor of Japan, November 2008 at the Marine Biological Laboratory. Photo by Tom Kleindinst.

This trip to Friday Harbor was the first of 18 more that the Shimomuras would make between 1961 and 1988, both to collect jellyfish specimens and for family recreation and relaxation. Their children soon joined in the netting operations, and the team collected and processed more than 850,000 specimens over the years. Osamu finally determined a structural model for the protein aequorin in the mid-1970s and a few years later did the same for the chromophore of GFP.

In 1981, Osamu accepted a position as senior scientist at the Marine Biological Laboratory, and the family left Princeton and built a new home in Falmouth. Osamu had earlier discovered that calcium triggers luminescence in aequorin; thus aequorin had become known as an excellent calcium probe for various research applications. The Shimomuras were practically the only source of purified aequorin, derived from their jellyfish specimens, and they received requests for it from laboratories around the world. Working at the MBL, Akemi took on the job of purifying both aequorin and GFP to accommodate research requests, which became a nearly full-time endeavor.

“Osamu Shimomura was the first ever to purify one important protein and substance after another that are responsible for bioluminescence (using a vast number of organisms that he personally collected). He selflessly supplied the purified material to scholars around the world. He and his wife, Akemi, kept to the bench for so many years without seeking glory or public recognition,” said the late MBL Distinguished Scientist Shinya Inoué, a longtime colleague and friend of the Shimomuras.

"We biologists are so lucky that Osamu Shimomura was with Akemi," said Tomomi Tani, a Japanese scientist who formerly worked at the MBL and was friendly with the Shimomuras. "Without Akemi, we might not be able today to see the fluorescence emission of GFP in live cell imaging," he said. 

The Shimomura lab at MBL also conducted research on other bioluminescent organisms, ranging from mushrooms to dinoflagellates to worms and brittle stars. In addition to her Aequorea work, Akemi worked on fungus bioluminescence and also purified luciferase, the enzyme responsible for bioluminescence, from the Norwegian jellyfish Periphylla.

In 1994, Martin Chalfie at Columbia University showed that GFP could be expressed in a bacterial cell, where its fluorescence illuminated the internal processes of the cell. This discovery led to a revolution in biological imaging, with GFP becoming an essential tool in biology, physiology, and medicine, especially as a fluorescent marker of proteins inside cells. In 2008, Osamu Shimomura, Martin Chalfie, and Roger Tsien were awarded the Nobel Prize in Chemistry for the discovery and development of GFP. Akemi, their children, and representatives of the MBL traveled with Osamu to Stockholm for the Nobel ceremonies in December.

Akemi traveled widely with her husband throughout their marriage, both for conferences and research expeditions and to visit their grown children. She also enjoyed exploring art galleries and loved the beauties of nature, often visiting Mt. Rainier and other scenic locations en route to Friday Harbor, and growing flowers and plants at her home. Akemi and Osamu formed many close friendships over the years, both in Japan and in the United States, and Akemi’s friends appreciated her intelligence, encouragement of others, and kindness.