Gene genesis

About a quarter of present-day life's DNA blueprint was sketched out by 2.8 billion years ago

Using the genetic equivalent of the Hubble telescope, researchers have peered into the distant past and witnessed an explosion of new genes that happened more than 3 billion years ago.

About 27 percent of all gene families that exist today were born between 3.3 billion and 2.8 billion years ago, two researchers from MIT report online December 19 in Nature. The surge of gene births — which the scientists have dubbed the Archean expansion — predate some important changes in Earth’s early chemistry, including the appearance of large amounts of oxygen in the atmosphere, say evolutionary biologists Eric Alm and Lawrence David.

The study may show how early organisms responded to and helped alter the planet’s chemistry. Daniel Segrè, a computational biologist at Boston University, says that the work provides “insight into really ancient metabolic events.” 

Fossils of organisms billions of years old are difficult to find; the earliest organisms might not have been preserved in stone at all. Most familiar fossils appeared in the Cambrian period more than 540 million years ago. Some stromatolites — fossils of cyanobacteria — are as much as 3.4 billion years old.

But the researchers have found a rich molecular fossil bed billions of years old in the genetic blueprints of living organisms.

“Imprinted in the DNA of modern organisms is the history of these Precambrian events,” says Alm.

To read that history, the researchers traced the evolution of 3,983 gene families in the genomes of 100 different living species. Gene families are groups of genes that share similar structures and functions. Analyzing that amount of data is a technical tour de force, says Jason Raymond of Arizona State University in Tempe. Most researchers painstakingly reconstruct the evolutionary history of one gene at a time, he says. By simultaneously examining how thousands of genes changed over time to produce the variation seen in organisms today, “they’ve leapfrogged other researchers,” he says. “If they’d have done this 10 years ago, I’d be out of a Ph.D.”

Genes for shuttling electrons burst onto the scene about 3.3 billion years ago, the researchers calculate. Those genes, known as electron transport genes, are important for such processes as photosynthesis and respiration. By increasing the energy efficiency of some early life forms, these genes may have enabled populations to thrive. 

Genes for using oxygen appeared at the tail of the genetic expansion around 2.8 billion years ago, long before oxygen began accumulating in the atmosphere around 2.5 billion years ago. The team also found evidence for the birth of genes for processing nitrogen and for using iron, molybdenum, copper and other elements.

While the genetic predictions match geochemical data for many of the elements, a few appear to contradict ideas about Earth’s early history. For instance, the new data predict that genes for using nickel were increasing at a time when geochemists say nickel concentrations in the ocean were crashing.

“Somebody’s wrong, and that’s what’s really exciting to me,” says Timothy Lyons, a geochemist at the University of California, Riverside. While he doesn’t expect the genetic models to singlehandedly overturn geochemical models of the early ocean, the new study might help refine chemical predictions. The genetic data is “another control and constraint that can’t be ignored.”

Tina Hesman Saey is the senior staff writer and reports on molecular biology. She has a Ph.D. in molecular genetics from Washington University in St. Louis and a master’s degree in science journalism from Boston University.

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