The “collective genome of all life” went through an expansion around 3 billion years ago that gave birth to 27 per cent of all the gene families that exist today, say two scientists from Massachusetts Institute of Technology (MIT) in the US.
They also believe they have detected the origin of the modern electron transport, an essential biochemical process for shuttling electrons across cell membranes and which characterizes the metabolism of oxygen-breathing organisms.
MIT computational biologists Eric Alm and Lawrence David traced thousands of genes from 100 modern genomes back to when they first appeared on Earth and used the results to create a “genomic fossil” that shows not only when the genes came into being but also which ancient microbes possessed them.
Palaeontologists describe the Cambrian Explosion, which lasted several millions of years and occurred about 580 million years ago, as a period of “rapid” change that spawned new life forms that eventually led to the diversity of animal life that we see today.
Fossils have helped scientists to map what has happened since the Cambrian Period, but the 3 billion years preceding it is somewhat of a mystery because cells from that time were soft-bodied and left hardly any fossil imprints.
However, one microscopic fossil of those times is available today in abundance, and that is DNA. All organisms inherit their genomes from previous generations, and so their DNA and RNA should contain an entire package of hereditary information.
Or as Alm and David put it, the “composition of modern-day genomes may bear imprints of ancient biogeochemical events”.
They reasoned that it should be possible to use modern-day genomes to reconstruct the evolution of our microbial ancestors.
A sort of “reverse engineering” (in the sense of going backwards through a development cycle) of modern-day genomes to find the one we all came from.
To do such a thing you need a model of how genes evolve, and this is where computational biology comes into the study.
Alm and David developed their own mathematical model of how genes evolve. Their “macroevolution” model takes into account a number of events at the level of the gene that causes genomes to vary as they pass down the generations.
The events include “gene birth” (a new gene is “born” and inherited), “gene transfer” (swapping genes between organisms, or transfer from one organism to another), “gene duplication” (the gene gets copied into the same genome), and “gene loss” (the gene simply does not get passed onto the next generation).
They combined the model with information from the ever-growing genome library to map the “evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline”.
Their results suggest there was a period between 3.3 and 2.8 billion years ago, which they have named the Archean Expansion, during which 27 per cent of all presently existing gene families were born.
” Surprisingly, we find that a brief period of genetic innovation during the Archaean eon, which coincides with a rapid diversification of bacterial lineages, gave rise to 27% of major modern gene families,” Alm and David wrote.
At first, because so many of the new genes they identified are connected to oxygen, they thought that the emergence of oxygen may have caused the Archean Expansion.
Oxygen first appeared in our planet’s atmosphere about 2.5 billion years ago, and there is a theory that as it accumulated, it probably killed off a lot of anaerobic life forms that did not use oxygen to make energy. That period has been termed the Great Oxidation Event.
Alm, a professor in the Department of Civil and Environmental Engineering and the Department of Biological Engineering at MIT, told the press that:
“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.”
But when they looked more closely at the results, they found that the oxygen-utilizing genes emerged towards the end of the Archean Expansion 2.8 billion years ago, which is more consistent with when geochemists believe the Great Oxidation Event took place.
So instead, Alm and David suggest they have discovered the point when modern electron transport, the biochemical means by which electrons are shuttled across cell membranes, was born.
“A functional analysis of genes born during this Archaean expansion reveals that they are likely to be involved in electron-transport and respiratory pathways,” they wrote.
All creatures that breathe oxygen use electron transport, and plants and some micro-organisms also use it in photsynthesis when they capture energy from the sun.
A type of photosynthesis called oxygenic photosynthesis is thought to be responsible for creating the oxygen that led to the Great Oxidation Event, and is responsible for the oxygen we breathe today.
If electron transport evolved during the Archean Expansion, it would have played an important role in the appearance of key oxygen-related biochemical processes that led to life as we know it, including photosynthesis and respiration, which together enable large amounts of energy to be captured and stored in our planet’s biosphere.
David, who recently received his PhD from MIT and is now a Junior Fellow in the Harvard Society of Fellows, said:
“Our results can’t say if the development of electron transport directly caused the Archean Expansion.”
“Nonetheless, we can speculate that having access to a much larger energy budget enabled the biosphere to host larger and more complex microbial ecosystems,” he added.
Alm and David also looked at how the microbial genes changed after the Archean Expansion. They found an increasing proportion of genes using oxygen, and coding for enzymes linked to copper and molybdenum, which is consistent with the geological record.
“Genes arising after this expansion show increasing use of molecular oxygen … and redox-sensitive transition metals and compounds, which is consistent with an increasingly oxygenating biosphere,” they wrote.
Andrew Knoll, a Harvard professor of natural history and expert in the paleontology and biogeology of the Archean and Proterozoic periods said:
“David and Alm have integrated genomics and phylogenetics in an innovative and stimulating way, shedding welcome light on the early evolution of life.”
“Hearteningly to Earth scientists, they paint a picture of metabolic evolution quite consistent with geologic expectation,” he added.
Alm said their study proves that “the histories of very ancient events are recorded in the shared DNA of living organisms.”
He said as we understand more about how to decode that DNA history, we should be able to reconstruct in great detail what happened in the early evolution of life on Earth.
“Rapid evolutionary innovation during an Archaean genetic expansion.”
Lawrence A. David and Eric J. Alm.
DOI: doi:10.1038/nature09649.
Additional source: MIT News (“Scientists decipher 3-billion-year-old genomic fossils”, Denise Brehm, 21-Dec- 2010).
Written by: Catharine Paddock, PhD