[cdn-nucl-l] D. radiodurans - potential to degrade radioactive materials and withstand high levels of radiation, sequenced

["Adam McLean" <adam.mclean@utoronto.ca>]

Posted on the Pacific Northwest National Laboratory's News & Information
web site on August 12, 2002 and at: 
http://www.pnl.gov/news/2002/02-26.htm

Adam

-----------------------

Release date: August 12, 2002 
Contact:  Mary Ace
(509) 372-4277 

PNNL gathers most complete protein map of "world's toughest bacterium"
RICHLAND, Wash.-Scientists at the Department of Energy's Pacific
Northwest National Laboratory have obtained the most complete protein
coverage of any organism to date with the study of a radiation-resistant
microbe known to survive extreme environments. This research potentially
could open up new opportunities to harness this microorganism, called
Deinococcus radiodurans, for bioremediation.

A study published in the Aug. 20 issue of the Proceedings of the
National Academy of Sciences observed a 61 percent coverage of the
microbe's possible predicted set of proteins, or its proteome. This is
the most complete proteome reporting to date of any organism. (The
proteome is the collection of proteins expressed by a cell under a
specific set of conditions at a specific time.) PNNL scientists
identified more than 1,900 proteins in D. radiodurans.

Studying the amount of each protein present at any time has become more
important as scientists attempt to learn which proteins are involved in
important cellular functions. DOE's Microbial Genome Program, an element
of the Genomes to Life Program, provided the genomic information for
various microorganisms, including D. radiodurans, and developed ways to
predict the set of possible proteins, which hold the key to why and how
these microbes carry out different functions.

D. radiodurans is of interest because of its potential to degrade
radioactive materials, its ability to withstand high levels of radiation
and its impressive DNA repair capabilities. The Guinness Book of World
Records once called it the world's toughest bacterium.

"We've been able to see more of the proteins, especially those proteins
that exist in small quantities," said Mary Lipton, PNNL senior research
scientist and lead author of the PNAS paper. "Because our coverage is
unprecedented, we're now able to provide biologists with protein-level
information they never had access to before."

To identify proteins involved in various functions, PNNL researchers
exposed D. radiodurans to several stresses and environments: heat shock;
cold shock; exposure to chemicals that damage DNA such as
trichloroethylene; exposure to ionizing radiation; and starvation. They
were able to identify many proteins previously only hypothesized to
exist on the basis of DNA information and also proteins that seemed to
have little function. New proteins that became active only during a
specific condition also were identified, as were proteins that appeared
to exist all the time.

To achieve this unprecedented coverage, researchers used a new
high-throughput mass spectrometer based on Fourier-transform ion
cyclotron resonance developed at PNNL. This instrumentation allows
scientists to identify thousands of proteins within hours. The system
relies on a two-step process that first uses tandem mass spectrometry to
identify biomarkers for each protein.

"We've not only identified the proteins, we have validated our results
by using two mass spectrometry techniques," said Richard D. Smith, PNNL
principal investigator.

"Once we've identified the protein biomarkers, then we never have to
repeat the identification step, thereby speeding up our experiments. As
a result we not only have a much more complete view of the proteome than
existed previously, but we also can follow changes to it much faster."

The experiments were conducted in the William R. Wiley Environmental
Molecular Sciences Laboratory, a DOE scientific user facility supported
by the Office of Biological and Environmental Research and located at
PNNL.

Other authors involved in the research came from Louisiana State
University and the Uniformed Services University of the Health Sciences
in Bethesda, Md.

Business inquiries on PNNL research and technologies should be directed
to 1-888-375-PNNL or e-mail: inquiry@pnl.gov.

Pacific Northwest National Laboratory is a DOE research facility and
delivers breakthrough science and technology in the areas of
environment, energy, health, fundamental sciences and national security.
Battelle, based in Columbus, Ohio, has operated the laboratory for DOE
since 1965.