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| Conceptual sketch of future metabolomics challenges and opportunities from May 2010 NSF-JST workshop on metabolomics. Click to enlarge. |
The US National Science Foundation (NSF) and Japan Science and Technology Agency (NSF-JST) have launched a joint program, Metabolomics for a Low Carbon Society (METABOLOMICS), and are soliciting research projects. The goal of this joint NSF-JST
program is to advance novel biological knowledge in metabolomics in the areas of energy and the environment, and to foster greater collaborative interactions between Japanese and US scientists in these priority areas.
The metabolome is the complete set of metabolites expressed within an organism, and reflects the networks of enzymatic pathways encoded within the genome as well as the interplay of developmental processes and a changing environment over the lifetime of the organism. Key goals of metabolomics research include 1) chemical annotation, i.e. determining the
chemical structure of each molecule; 2) biological annotation, i.e. connecting each metabolite to a specific enzyme, biochemical pathway, or
biological process; and 3) metabolomic annotation, i.e. the distribution of each metabolite in different cells of an organism which includes spatial and temporal information as well as concentration.
Metabolomics has exciting applications in bioenergy, environmental interactions, functional genomics and gene discovery, secondary metabolism, genome-wide association mapping, systems biology and metabolic modeling in plant, algal, and microbial systems. However,
the scientific promise of metabolomics currently faces multiple challenges that need to be addressed. These challenges include: how to define the metabolome, metabolite annotation, standardization, spatially and temporally resolved sampling, measurement of metabolite flux, dynamic range and depth-of-coverage, instrumentation and infrastructure, informatics and databases.
…The goal of this joint program is to support collaborative research among US and Japanese scientists focused on fundamental research
that contributes to a broader understanding of the metabolic processes in plants, algae or microbes as they relate to bioenergy and the
environment. The outcomes of these projects are anticipated to contribute to improved annotation and standardization of metabolites in
these organisms. Projects are expected to involve at least one US and one Japanese principal investigator in a single coordinated
research project.—Program announcement
NSF anticipates that up to four awards will be made in FY 2011, pending availability of funds, with a total of US$2 million available in FY2011. NSF also anticipates that approximately $12 million in total, over 3 years, will be available from NSF and JST to support awards made under this competition. Of this
total, $6 million is anticipated to be available from NSF, pending appropriation of funds, to support US researchers recommended for awards, and the remainder will be equivalent JST resources to support the Japanese researchers recommended for funding.
NSF and JST had held a joint workshop in May 2010 to identify and prioritize key strategic areas for metabolomics research. Japan has invested heavily in metabolomics, NSF noted, and said they are ideal
partners for collaborative research in plant, algal, and microbial metabolomics. One of the topics explored at the workshop was biofuels and food.
A report summarizing the different sessions noted of the bioenergy and food session that plants produce an enormous diversity of metabolites of economic importance. The uses of the metabolites are also very diverse, including nutrients and medicines, mediators of environmental stress adaptation, energy sources, and chemical feed stocks.
Optimizing production of energy-rich biofuel molecules involves increasing production of abundant plant components, such as starch, sugars, cellulose, and oils, while keeping inputs of fertilizer and water low. Transformation of these ‘primary’ products of plant biosynthetic pathways by microorganisms (e.g. fermentation) is often necessary to convert biomass to industrially useful products, such as ethanol and butanol, to desirable food and medicinal products.
—Workshop report
The session identified three areas of possible research focus:
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Elucidate limiting steps and regulatory components (understanding biochemical mechanisms) in
biofuel and food production: An integrated combination of metabolomics, including genetic
manipulation, transcriptional analysis, and analysis of physiological phenotypes can provide information
required to engineer changes leading to increases in biomass and in levels of specific components. The
integrated technologies can provide critical information for identifying limiting enzymatic or transport
steps, regulatory compounds and their targets, the location and timing of metabolite production within
plants, and novel pathways. -
Identify specific target compounds related to optimal properties (independent of understanding
mechanism) of crops, food, and fuel products: ‘Green’ initiatives such as the movement towards
widespread utilization of perennial energy crops and multi-culturing of crops have promise for
sustainability of agriculture, but there is lack of clarity about the chemistry involved in these processes
and how the chemistry relates to optimization of these practices. Similarly, the chemistry involved in
cooking and fermentation for both food and fuel production is complex with many uncharacterized
metabolites. Because of the complexity of the plant metabolome and the products of microbial
conversion, successful development of biofuels and improvements in food quality and quantity will
require highly sensitive and high-resolution metabolomics technologies, as well as comprehensive
untargeted analysis and statistical approaches. Development of high-throughput methods are needed
for biologists to use in measuring identified targets in breeding populations, transgenic lines, samples
from the environment, unprocessed and processed food products (e.g. GMO products), etc -
Training and existing mechanisms: Training is a bottleneck in development of metabolomics for
improvement of plant quality and quantity. In particular, there is a need to improve training in
chemistry, biochemistry, and computational approaches and to recruit students into plant biology.
Existing NSF programs, including the IGERT program and existing Japanese programs could be used to
improve plant biochemistry interest and background. There is interest in exchange programs for
students, fellowships for undergraduate and graduate students, and course development. Additionally,
the NSF RCN mechanism could be used to coordinate US and Japanese researchers in food and biofuel
biochemistry.
Resources
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May 2010 Workshop held at the University of California, Davis, to discuss challenges in metabolomics