Director, Institute of Environmental Microbiology, Kyowa Kako Co., Ltd.
Attracted to thermophilic bacteria
— From the mechanism for the thermostability of proteins to the origin of life —
Organisms often live in places which seem unlivable. For instance, thermophilic bacteria live in and around hot springs and deep-sea hydrothermal vents where temperatures can exceed 100ºC. Prof. Oshima wondered how they can live in an environment with such high temperatures and what factors determine the temperature limit for life. He has been looking at the structures of proteins for the answers.
Prof. Oshima first learned thermophilic bacteria at NASA’s Ames Research Center. After returning to Japan, he began isolating thermophilic bacteria and analyzing the structures and functions of their proteins because he wanted to determine how they can survive at such high temperatures. In 1968, he isolated a new type of thermophilic bacterium from a hot spring in Izu and named it “Thermus thermophilus”. It has a growth temperature that is greater than 80ºC, which was the highest growth temperature for thermophilic bacteria at that time. He found that its body length of 2 µm and the structure of its cell envelope are very similar to Escherichia coli, which is widely used in biochemical research. Therefore, it can be compared to Escherichia coli, and, like E. coli, it is also suitable for the gene manipulation at high temperatures.
After Prof. Oshima found that the thermostability of transfer RNA in thermophilic bacteria is caused by a slight difference in the base pairs, his interest shifted to modifying proteins to increase thermostability. However, it is extremely difficult to design proteins with the proper conformation to make them thermally stable. So, he employed “directed evolution”, in which forced evolution is used in order to obtain functions for specific purposes by introducing a mutation into a protein-encoding gene. A gene is extracted from a mesophile such as E.coli or Bacillus subtilis, and is introduced into a chromosome of the thermophilic bacterium, and the resulted transformant is then grown at elevated temperatures. Only strains in which the integrated gene is mutated to encode a thermally stable protein can grow, and thus, he was able to modify the thermostability of the proteins by screening strains in this way.
Thermophilic bacteria are a key to the birth of living organisms in the primordial earth. The comparison of the base sequences of the ribosomal RNA, which all living organisms have in common, has shown that thermophilic bacteria are the dominant organism near the root of the evolutionary tree. Prof. Oshima thinks that they could be the origin of all living organisms. He calls them the “commonote,” or universal ancestor. In order to speculate the nature of the commonote, he researched the common characteristics of all hyperthermophilic bacteria that grow at temperatures higher than 90ºC. However, they do not always have the same characteristics as their ancestors because existing hyperthermophilic bacteria have diverged during 4 eons of evolution. He expects to discover more about the commonote from the “Ocean Drilling Program” of the Japan Marine Science and Technology Center (currently, Japan Agency for Marine-Earth Science and Technology), in which researchers will drill 4,000 m below the sea floor. The temperature around a hydrothermal vent is higher than 100ºC in some places, and many scientists believe that the environment around the vent is close to the environment during the birth of all living organisms. He says, “We know that there are living organisms in the geosphere below the sea floor, and there may be an unimaginable number of living organisms there.”
T. thermophilus that Prof. Oshima discovered has been kept in culture collections around the world as a usable thermophilic bacterium. Currently, thermophilic bacteria are used in research projects on protein structural genomics, which many countries perform. Japan’s National Project on Protein Structural Genomics “Protein 3000” is one of those research projects. DNA polymerase, used for the polymerase chain reaction (PCR), which is an artificial DNA-copying technology used in molecular therapy, gene diagnosis and research on cancer, is also an enzyme originating from thermophilic bacteria. Thermophilic bacteria are used in many fields because of their thermostability. He said, “A few decades ago, nobody even thought that they would have applications in medical fields. Things may turn out unexpectedly good like my research on thermophilic bacteria. So, you should research what interests you most.” He has also recently focused on compost. There is compost, supplied from a compost factory for sewage-treatment, on his lab’s deck. “It was thought that the highest temperature of fermenting compost was around 75 to 80ºC, but the temperature of our compost is higher than 90ºC. We will find new bacteria that have not been written about in the textbooks and literatures,” says Prof. Oshima with a smile. There may be more unexpected results from this compost research.
