Modern-day genomes used to reconstruct evolution of 3bn-yr-old microbes

WASHINGTON - MIT scientists have used modern day genomes to reconstruct the evolution of ancient microbes.

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.

About 580 million years ago, life on Earth began 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.

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.

Because so many of the new genes they identified are related to oxygen, Eric Alm, a professor in the Department of Civil and Environmental Engineering and the Department of Biological Engineering, and Lawrence David, who is now a Junior Fellow in the Harvard Society of Fellows, 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 anerobic life forms in the Great Oxidation Event.

Analysis 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. The two scientists believe they’ve detected the birth of modern electron transport, the biochemical process responsible for shuttling electrons within cellular membranes. Electron transport is used to breathe oxygen and by plants and some microbes 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. Nonetheless, we can speculate that having access to a much larger energy budget enabled the biosphere to host larger and more complex microbial ecosystems,” said David.

They investigated 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.

“What is really remarkable about these findings is that they prove that the histories of very ancient events are recorded in the shared DNA of living organisms. And now that we are beginning to understand how to decode that history, I have hope that we can reconstruct some of the earliest events in the evolution of life in great detail,” said Alm. (ANI)