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Bacterial 'nano-machines' are focus of $15M grant

Scientists from MIT, Harvard University, and Brigham and Women's Hospital have received $15 million from the Department of Energy to study three bacteria to understand the natural roles they play in sustaining the biosphere and for their potential as "nano-machines" to clean the environment and produce energy.

The five-year grant announced today is part of the DOE's $103 million Genomes to Life Program. The 10-year goal of the program is to take advantage of solutions nature has already devised to help solve a variety of problems. Through biological, physical and computational sciences, the program seeks to understand entire living organisms and their interactions with the environment.

The researchers, using the previously determined genome or genetic makeup of each organism, will set out to define each organism's proteome, or the unique interactions of its proteins. They will also examine each organism's ecology, or the interrelationships of the organisms to their environments.

By studying both systems, they hope to learn how to further engineer each microorganism to handle hazardous chemical waste and other environmental concerns. They could also be engineered as possible energy sources.

Professor Penny Chisholm, a co- principal investigator on the grant, emphasized that "genomics approaches are also extremely valuable for helping us understand the structure of natural microbial ecosystems, and the role they play in sustaining the earth's biogeochemical cycles.

"These cells do not exist in a vacuum; their metabolic networks have been shaped over evolutionary time by interactions with other organisms. We have to understand their ecology if we are to gain a full understanding of their cellular architecture."

George Church, a professor of genetics at Harvard Medical School and at the Harvard-MIT Division of Health Sciences and Technology, will head the team.

"It's very exciting being part of such a truly interdisciplinary team applying computational biology and genomics to the urgent issues of global energy and ecology," Church said.

MIT members of the team include Chisholm, the McAfee Professor in Engineering who has appointments in the Departments of Civil and Environmental Engineering (CEE) and Biology; and Martin Polz, CEE's Henry L. and Grace Doherty Professor in Ocean Utilization.


The researchers will examine the bacteria Prochlorcoccus, Pseudomonas and Caulobacter. Prochlorococcus, a simple blue-green algae, is involved in 40 percent of the photosynthesis in the oceans, removing from the atmosphere carbon dioxide - which is linked to global warming - and producing oxygen. Pseudomonas, while a member of a family of significant human pathogens, is also one of the most versatile biochemical factories on Earth. It can conduct more different chemical reactions than almost any other organism, and could handle a variety of toxic wastes. Caulobacter is known as a scavenger of compounds, especially in low concentrations of water.

"These microorganisms can be thought of as nano-machines," said Church. "By knowing their genomes as we do, we have a linear computer tape, or code, that in principle tells us how to assemble the machines. But we need to study the machines themselves, to move beyond a one-dimensional understanding to a three-dimensional view to learn how we can help the machine to do the right thing for humans and the ecosystem."

A version of this article appeared in MIT Tech Talk on August 14, 2002.

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