[ RadSafe ] News Article: Ancient microbes repair DNA

Wed Aug 29 06:55:14 CDT 2007

For those interested in radiation effects, and gene
damage and repair, nothing new.  

http://www.the-scientist.com/news/home/53546/

-----------------
Bacteria trapped in permafrost breathe and repair
their DNA for more than half a million years
[Published 28th August 2007 04:13 PM GMT]

Bacteria frozen in permafrost for hundreds of
thousands of years slowly respirate and repair their
DNA, according to a report in the Proceedings of the
National Academy of Sciences this week. The strategy
may explain how life persists over geologic time
scales, the authors say. 

Other scientists have claimed to recover viable
microbes that have been trapped in amber, salt or
buried deep within the earth for tens to hundreds of
millions of years, but how these ancient bacteria
remained alive for so long under extreme conditions
has remained a mystery. 

Researchers have postulated that they persist as
dormant endospores in which metabolic activity has all
but ceased. But those resting cells would still be
buffeted by physical and chemical degradation, said
Eske Willerslev of the University of Copenhagen in
Denmark, who led the current effort. DNA, in
particular, would become fragmented unless it could be
repaired. 

"Many people, including myself, have been very
skeptical about [those] results," Willerslev told The
Scientist. "There has not been a mechanism to explain
how cells could survive for that long." 

His team collected ice cores up to a million years old
from the permafrost of Antarctica, Siberia and
Canada's Klondike, and placed them chambers chilled to
-10 degrees C and filled with an atmosphere free of
carbon dioxide. After waiting three months for CO2
trapped in air bubbles to dissipate, they collected
gas emitted by the cores for another six months.
Samples older than 600,000 years were inert, they
found, but younger samples generated carbon dioxide -
a sign of life. 

Previous work had shown that strands of DNA amplified
from dead microbial fossils rarely exceed 500 base
pairs, but the group targeted fragments 4,000 base
pairs long. To estimate the integrity of the microbial
DNA, they used an enzyme to break DNA strands at
damaged regions. Even in samples pre-digested with the
enzyme, the DNA was sufficiently well-preserved for
the researchers to amplify 4,000 base-pair strands in
the younger samples, evidence of active DNA repair. 

To make sure they were not amplifying DNA of modern
bacteria contaminating the ancient samples, the
researchers conducted all experiments in two labs. The
paired findings agreed: Samples younger than 600,000
years old yielded long strands of DNA, while older
ones yielded only shorter scraps. 

The team matched the amplified sequences to known
groups of bacteria, and found that the variety of
microbes diminished as the ice got older. "What I
think we are seeing is a community that is slowly
dying out," Willerslev said. The oldest intact DNA
they recovered mostly matched sequences for
Actinobacteria, a phylum not known to form endospores,
suggesting that slow metabolism and repair were key to
longevity. 

Finding enough energy to continue a low level of
activity shouldn't be a problem, even in ice, said P.
Buford Price of the University of California,
Berkeley, who was not involved with the study. His
past findings suggested that thin films of water, just
a few molecules deep between the ice crystals, would
be enough to transport nutrients from dust trapped in
the permafrost, he told The Scientist. 

Price said he had "serious doubts" about earlier
claims of ancient microbes, which could have been
artifacts of contamination, but found the present
study credible. "I believe it," he said. "Willerslev
argues forcefully that a better strategy for microbes
to survive is not to go dormant, but to stay
metabolically active and use that energy to repair
DNA." 

Such survival "seems plausible," said Jeffrey Bada of
the University of California, San Diego, who has
developed probes for frozen Martian life for NASA.
Bada, who was not a coauthor of the study, noted that
cold temperatures slow chemical degradation, which
would allow even sluggish repair to keep up. 

Willerslev said the findings may help study the
possibility of life beyond Earth. Both Mars and
Jupiter's icy moon Europa are much colder than Earth's
permafrost, and may harbor torpid life. 

Susan Brown 
mail at the-scientist.com 

Links within this article: 

S.S. Johnson et al., "Ancient bacteria show evidence
of DNA repair," PNAS, August 27, 2007. 
http://www.pnas.org 

R.J. Cano and M.K. Borucki, "Revival and
identification of bacterial spores in 25- to
40-million-year-old Dominican amber," Science, May 19,
1995. 
http://www.the-scientist.com/pubmed/7538699 

R.H. Vreeland et al., "Isolation of a 250
million-year-old halotolerant bacterium from a primary
salt crystal," Nature, October 19, 2000. 
http://www.the-scientist.com/pubmed/11057666 

K.D. Bidle et al., "Fossil genes and microbes in the
oldest ice on Earth," PNAS, August 14, 2007. 
http://www.the-scientist.com/pubmed/17686983 

H. Black, "Extremophiles: They love living on the
edge," The Scientist, July 8, 2002. 
http://www.the-scientist.com/article/display/13150/ 

Eske Willerslev 
http://www.dna.gfy.ku.dk/ew/ew.html 

M. Höss, et. al., "DNA damage and DNA sequence
retrieval from ancient tissues," Nucleic Acids
Research, April 1,1996. 
http://www.the-scientist.com/pubmed/8614634 

P. Buford Price 
http://www.physics.berkeley.edu/research/price 

P.B. Price and T. Sowers, "Temperature dependence of
metabolic rates for microbial growth, maintenance, and
survival," PNAS, Mar 30, 2004. 
http://www.the-scientist.com/pubmed/15070769 

Jeffrey L. Bada 
http://exobio.ucsd.edu/bada.htm 

+++++++++++++++++++
"All of the old-timers knew that subprime mortgages were what we called neutron loans --  they killed the people and left the houses. . . .
"LOUIS S. BARNES, a partner at Boulder West, a mortgage banking firm.

-- John
John Jacobus, MS
Certified Health Physicist
e-mail:  crispy_bird at yahoo.com

____________________________________________________________________________________
Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. 
http://answers.yahoo.com/dir/?link=list&sid=396545433