Scientists date prehistoric bacterial invasions still present in today’s cells

Long before Earth became lush, when life consisted of single-celled organisms afloat in a planet-wide sea, bacteria invaded the ancient ancestors of plants and animals and took up permanent residence. One bacterium eventually became the mitochondria that today power all plant and animal cells; another became the chloroplast that turns sunlight into energy in green plants.

A new analysis by two University of California, Berkeley, graduate students more precisely pinpoints when these life-changing invasions occurred, placing the origin of photosynthesis in plants hundreds of millions of years earlier than once thought.

“When you are talking about these really ancient events, scientists have estimated numbers that are all over the board,” said coauthor Patrick Shih. Estimates of the age of eukaryotes – cells with a nucleus that evolved into all of today’s plants and animals – range from 800 million years ago to 3 billion years ago.

“We came up with a novel way of decreasing the uncertainty and increasing our confidence in dating these events,” he said. The two researchers believe that their approach can help answer similar questions about the origins of ancient microscopic fossils.

Shih and colleague Nicholas Matzke, who will earn their Ph.Ds this summer in plant and microbial biology and integrative biology, respectively, employed fossil and genetic evidence to estimate the dates when bacteria set up shop as symbiotic organisms in the earliest one-celled eukaryotes. They concluded that a proteobacterium invaded eurkaryotes about 1.2 billion years ago, in line with earlier estimates.

They found that a cyanobacterium – which had already developed photosynthesis – invaded eukaryotes 900 million years ago, much later than some estimates, which are as high as 2 billion years ago.

Previous estimates used hard-to-identify microbial fossils or ambiguous chemical markers in fossils to estimate the time when bacteria entered ancestral eurkaryotic cells, probably first as parasites and then as symbionts. Shih and Matzke realized that they could get better precision by studying today’s mitochondria and chloroplasts, which from their free-living days still retain genes that are evolutionarily related to genes currently present in plant and animal DNA.

“These genes, such as ATP synthase – a gene critical to the synthesis of the energy molecule ATP – were present in our single-celled ancestors and present now, and are really, really conserved,” Matzke said. “These go back to the last common ancestor of all living things, so it helps us constrain the tree of life.”

Since mitochrondrial, chloroplast and nuclear genes do not evolve at exactly the same rate, the researchers used Bayesian statistics to estimate the rate variation as well as how long ago the bacteria joined forces with eukaryotes. They improved their precision by focusing on plant and animal fossils that have more certain dates and identities than microbial fossils.

The paper appeared online on June 17 in advance of publication in the journal Proceedings of the National Academy of Sciences. Matzke also is a member of UC Berkeley’s Center for Theoretical Evolutionary Genomics.


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