technologies, and help explain how microbes shape Earth's climate
web version:
http://newscenter.lbl.gov/news-releases/2010/07/18/microbial-world-unmapped/
Contact: Dan Krotz, dakrotz@lbl.gov (510) 486-4019
A new way of surveying microbes for the metals they contain reveals that
biologists have been relying on the equivalent of a 15th century map of
the world.
It turns out that there are many more metal-containing proteins in
microbes than previously recognized.
This means the microbial world boasts a broader and more diverse array
of metal-driven chemical processes than scientists have imagined. In
fact, most have yet to be discovered, according to a first-of-its-kind
survey of the metals in three microbes conducted by scientists from the
U.S. Department of Energy's Lawrence Berkeley National Laboratory in
collaboration with scientists at the University of Georgia.
Their research will help chart a more complete understanding of the
far-reaching roles of metals in biology and the Earth's climate. It
could also lead to new ways to harness metal-driven chemical processes
to create next-generation biofuels or to clean up environmental
contaminants.
Microbes assimilate metals from their environment and incorporate them
into proteins in order to power life's most important chemical
processes, such as photosynthesis, respiration, and DNA repair.
Metal-containing proteins in microbes also helped oxygenate the planet's
atmosphere billions of years ago, enabling life as we know it, and they
continue to play a critical role in the Earth's carbon cycle.
But the diversity and extent of microbial metals had eluded scientists
until now.
"This is a huge surprise. It reveals how naive we are about the wide
range of chemistries that microbes do," says John Tainer of Berkeley
Lab's Life Sciences Division and the Scripps Research Institute in La
Jolla, CA. Tainer conducted the research with Michael Adams of the
University of Georgia and a team of scientists that includes Steven
Yannone and Gary Siuzdak of Berkeley Lab's Life Sciences Division.
The scientists report their research July 18 in an advance online
publication of the journal Nature.
Using state-of-the-art techniques, the team catalogued the metals in
three microbes: one that lives in human intestines, one plucked from a
hotspring in Yellowstone National Park, and one that thrives in the
near-boiling waters of undersea thermal vents.
They uncovered a microbial world far richer in metals than ever
expected. For example, in the undersea thermal-vent loving microbe, or
Pyrococcus furiosus, they found metals such as lead, manganese, and
molybdenum that P. furiosus wasn't known to use.
The scientists traced these newfound metals to the proteins that contain
them, called metalloproteins. They discovered four new metalloproteins
in the microbe, which increased the number of known metalloproteins in
P. furiosus by almost a quarter. Their discovery also increased the
number of nickel-containing enzymes in all of biology from eight to ten.
A similar survey of the other two microbes unearthed additional
unexpected metals and new metalloproteins. Based on this sizeable haul
from only three microbes, the team believes that metalloproteins are
much more extensive and diverse in the microbial world than scientists
realized.
"We thought we knew most of the metalloproteins out there," says Tainer.
"But it turns out we only know a tiny fraction of them. We now have to
look at microbial genomes with a fresh eye."
The team used a first-of-its-kind combination of two techniques to
envisage this uncharted microbial landscape. Biochemical fractionation
enabled them to take apart a microbe while keeping its proteins intact
and stable, ready to be analyzed in their natural state. Next, a
technology called inductively coupled plasma mass spectrometry allowed
them to identify extremely low quantities of individual metals in these
proteins.
Together, these tools provide a quick tally of the metalloproteins in a
microbe.
The current way to discover metalloproteins is much slower. Simply
stated, it involves genetically sequencing a microbe, identifying the
proteins encoded by its genes, and structurally characterizing each
protein.
"Standard methods of identifying metalloprotiens can take years," says
Yannone. "By directly surveying all microbial proteins for metals we
can rapidly identify the majority of metalloprotiens within any cell."
In addition to gaining a better understanding of the biochemical
diversity of microbes, the team's new metal-hunting technique could
expedite the search for new biochemical capabilities in microbial life
that can be harnessed for clean energy development, carbon
sequestration, and other applications.
"If you want to degrade cellulose to make biofuel, and you know the
enzymes involved require a specific metal-driven chemistry, then you can
use this technique to find those enzymes in microbes," says Yannone.
Adds Tainer, "Knowing that all of these metal-containing proteins are
out there, waiting to be found, is kind of like being in a candy store.
We might discover new proteins that we can put to use."
The research was funded by the Department of Energy Office of Science.
Berkeley Lab scientists provided the inductively coupled plasma mass
spectrometry equipment. They contributed to the experimental design and
data analysis in collaboration with University of Georgia scientists.
Lawrence Berkeley National Laboratory provides solutions to the world's
most urgent scientific challenges including clean energy, climate
change, human health, and a better understanding of matter and force in
the universe. It is a world leader in improving our lives and knowledge
of the world around us through innovative science, advanced computing,
and technology that makes a difference. Berkeley Lab is a U.S.
Department of Energy (DOE) national laboratory managed by the University
of California for the DOE Office of Science. Visit our website:
http://www.lbl.gov/
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