Scientists decipher 3-billion-year-old genomic fossils
Original source: MIT News
December 21, 2010
By Denise Brehm
About 580 million years ago, life on Earth entered a rapid period of change
called the Cambrian Explosion, a period defined by the birth of new life forms
over many millions of years that ultimately helped bring about the modern
diversity of animals. Fossils help palaeontologists chronicle the evolution of
life since then, but drawing a picture of life during the 3 billion years that
preceded the Cambrian Period is challenging, because the soft-bodied Precambrian
cells rarely left fossil imprints. However, those early life forms did leave
behind one abundant microscopic fossil: DNA.
Because any living organism inherits its genome - the entire package of
hereditary information existing in an organism's DNA and RNA - from ancestral
genomes, computational biologists at MIT reasoned that they could use modern-day
genomes to reconstruct the evolution of ancient microbes. They combined
information from the ever-growing genome library with their own mathematical
model that takes into account the ways that genes evolve: New gene families can
be born and inherited; genes can be swapped or horizontally transferred between
organisms; genes can be duplicated in the same genome; and genes can be lost.
The scientists traced thousands of genes from 100 modern genomes back to those
genes' first appearance on Earth to create a genomic fossil telling not only
when genes came into being but also which ancient microbes possessed those
genes. The work, reported in the Dec. 19 online issue of Nature, suggests that
the collective genome of all life underwent an expansion between 3.3 and 2.8
billion years ago, during which time 27 percent of all presently existing gene
families came into being.
Eric Alm, a professor in the Department of Civil and Environmental Engineering
and the Department of Biological Engineering, and Lawrence David, who recently
received his PhD from MIT and is now a Junior Fellow in the Harvard Society of
Fellows, have named this period the Archean Expansion.
Because so many of the new genes they identified are related to oxygen, Alm and
David first thought that the emergence of oxygen might be responsible for the
Archean Expansion. Oxygen did not exist in the Earth's atmosphere until about
2.5 billion years ago when it began to accumulate, likely killing off vast
numbers of anaerobic life forms in the Great Oxidation Event.
"The Great Oxidation Event was probably the most catastrophic event in the
history of cellular life, but we don't have any biological record of it," says
Closer inspection, however, showed that oxygen-utilizing genes didn't appear
until the tail end of the Archean Expansion 2.8 billion years ago, which is more
consistent with the date geochemists assign to the Great Oxidation Event.
Instead, Alm and David believe they've detected the birth of modern electron
transport, the biochemical process responsible for shuttling electrons within
cellular membranes. All organisms that breathe oxygen use electron transport to
do so, while plants and some microbes use electron transport during
photosynthesis when they harvest energy directly from the sun. A form of
photosynthesis called oxygenic photosynthesis is believed to be responsible for
generating the oxygen associated with the Great Oxidation Event, and is
responsible for the oxygen we breathe today.
The evolution of electron transport during the Archean Expansion would have
enabled several key stages in the history of life, including photosynthesis and
respiration, both of which could lead to much larger amounts of energy being
harvested and stored in the biosphere.
"Our results can't say if the development of electron transport directly caused
the Archean Expansion," says David. "Nonetheless, we can speculate that having
access to a much larger energy budget enabled the biosphere to host larger and
more complex microbial ecosystems."
The scientists went on to investigate how microbial genomes evolved after the
Archean Expansion by looking at the metals and molecules associated with the
genes and how those changed in abundance over time. They found an increasing
percentage of genes using oxygen, and enzymes associated with copper and
molybdenum, which is consistent with the geological record of evolution.
"David and Alm have integrated genomics and phylogenetics in an innovative and
stimulating way, shedding welcome light on the early evolution of life," says
Andrew Knoll, a Harvard professor of natural history whose own research focus is
Archean and Proterozoic paleontology and biogeology. "Hearteningly to Earth
scientists, they paint a picture of metabolic evolution quite consistent with
Alm says the findings "prove that the histories of very ancient events are
recorded in the shared DNA of living organisms." With scientists now beginning
to understand how to decode that history, he says he is hopeful that some of the
earliest events in the evolution of life can be reconstructed in great detail.