Pushing boundaries and helping to feed the world
11 July 2008 (Volume 3 Issue 7)
The field of plant science grows more important with every passing year, as increases in human populations and environmental pressures put stress on our ability to feed ourselves and maintain our environment.
The RIKEN Plant Science Center (PSC), located at the RIKEN Yokohama Institute, is at the forefront of this crucial field, as one of the world’s leading research centers in plant genomics, metabolomics, and other areas of plant science.
“The primary concept of our research is to promote plant science that is useful for society, mainly agriculture, environment, energy biomass and studies related to human health,” notes PSC Director Kazuo Shinozaki. “Of course, our research is basic, using model plants, but the focus is on useful genes for applications.”
By any measure, the PSC has been a great success during its eight years in existence. Plant science is one of the top fields at RIKEN, and the PSC is now one of the top research centers in plant science in the world—its researchers publish over 500 articles a year, and the center is ranked number two in the world, based on citations in scientific journals.
Research at the PSC concentrates on four major topics—metabolomics, the study of the complicated plant metabolic network; systems biology, or how plants regulate stress responses, disease resistance and metabolism; gene discovery, in which researchers tease out genes and their functions; and comparative genomics, finding parallels between the genetic data on model plants, such as Arabidopsis and poplar, and other plants, such as crops and trees, to see if the data can be applied to enhance productivity, drought and disease resistance, and other useful traits.
“Plants actually have very complex metabolic systems. In the plant kingdom there are 200,000 metabolites, compared with 2,500 in humans, for example,” says Shinozaki. “Since we established the metabolomics platform, we have collected a variety of mass spectrometric and nuclear magnetic resonance data and used it to analyze complex plant metabolomics and metabolic networks.”
Kazuki Saito, director of the Metabolomics Research Group, the group responsible for setting up the metabolomics research platform, is excited about the possibilities of the new platform, including the ability to investigate hundreds of different metabolites at a time, and to see how they interact with each other. “This is totally new work, metabolite–metabolite correlation—we never considered this before, how these compounds intensify each other,” he points out.
For the future, Saito says, “Our next challenge should be to intensify the power of the metabolome analytical platform, and integrate it with bioinformatics.” He adds that the group should work toward the advance of system biology, with mathematical models, but based more on holistic data sets, like transcriptome, metabolome and proteome data, to see in finer and finer detail how living organisms behave.
The center has seven groups analyzing plant functions—metabolomics, gene discovery, growth regulation, metabolic function, plant productivity systems, plant immunity and plant functional genomics. “The PSC has some of the best research infrastructure in the world in this area of research in that we can use gas and liquid chromatography and combined mass spectrometry for the analysis,” says Saito. “We also have access to four nuclear magnetic resonance machines, which we use for protein analysis.”
Plant science, like most scientific endeavors, is a collaborative activity, and joint ventures between scientists and institutes are crucial. So PSC is actively pursuing collaborations with research institutes both within Japan and overseas, including: the Max Planck Institute at Golm, Germany, with which RIKEN shares a database; the Chinese Academy of Science for work on rice and tree biotechnology; and the University of Pretoria for research concerning pharmaceuticals derived from Artemisia.
In charge of the internationalization effort is Ken Shirasu, leader of the Plant Immunity Research Team. Having spent most of his career doing research overseas, including at the Salk Institute in the US and the John Innes Center in the UK, Shirasu is well aware of the needs and concerns of international researchers.
Among its many international collaborations, his lab is working with the Sudan Agricultural Institute on research into Stryger, a parasitic plant that has infested and destroyed corn crops in large areas of Africa, especially Sudan. “It can be eradicated by brute force, by digging it up with machines, but in Africa farmers can’t afford such methods. So an inexpensive genetic solution could improve the lives of thousands of people there,” he explains.
One change that Shirasu is insisting on is the use of English in the lab, including seminars, lab meetings, and labels on equipment, even down to the trash cans. “In science you have to have good skills in English. You might have great science, but if you can’t present it, nobody will listen.”
A perceived language barrier can also discourage foreign researchers from coming here. “If people can’t communicate, they can’t discuss their work, and this is very important in the world of science,” Shirasu says.
As part of its efforts to make itself more foreign-researcher-friendly, the PSC decided to employ two non-Japanese team leaders this year, from South Korea and Vietnam, both with research backgrounds in the US.
“The best way to spread the word about the center is to exchange students—they’re the best advertising for us,” Shirasu points out. “They may come back someday and do research, and they will certainly talk about their experiences with their colleagues.”
Marco Trujillo
In plant immunity, the tagging of proteins with ubiquitin, which can lead to degradation, is emerging as a key regulatory process. German-born Marco Trujillo is investigating the mechanisms by which the attachment of ubiquitin to specific target proteins regulates plant immune responses, which are triggered by the detection of microbial pathogens.
“I focus on a specific kind of E3 ubiquitine ligase,” says Trujillo. “These contain a so called u-box domain, and we call them plant u-box proteins or simply PUBs.” He adds that by acting as scaffolds, they mediate the binding of ubiquitin to a target protein. “The tagging of a protein with ubiquitin can lead to several outcomes, for example degradation, relocalization to another compartment in the cell, endocytosis, and many others.”
Trujillo has employed, among others, a reverse-genetics approach using mutant ‘knock-out’ lines of Arabisopsis thaliana. “When we analyzed the knock-outs of certain PUBs, we found that they became more resistant to bacteria and other pathogens, and their responses were hyperactivated, but not constitutively, as is typical for most known negative regulators of immunity.”
“Knocking out these genes enhanced resistance, indicating that they act as negative regulators,” he adds. He explains that plants have both positive and negative regulators to keep their defenses tightly controlled. “A balanced response is needed: too much is deleterious for the plant; not enough makes it susceptible to attack by pathogens.”
Trujillo came to Japan in 2006, after working with Ken Shirasu at the Sainsbury Laboratory in England. His experience here has been a valuable one, both personally and scientifically. “RIKEN is well known for having good facilities. You can get anything you want here, any equipment you need, and I’ve had a lot of liberty to pursue my own research,” he says. “I was worried at first about the language barrier, but Dr. Shirasu insists that everyone speaks English in his lab, which allows for free scientific discussions.”
Trujillo is heading back to Germany later this year, to continue his work at Julius-Maximilians University, but he plans to continue his close collaboration with Shirasu, and with RIKEN.
