Gene swap key to evolution

Horizontal gene transfer accounts for the majority of prokaryotic protein evolution

Microbes evolve predominantly by acquiring genes from other microbes, new research suggests, challenging previous theories that gene duplication is the primary driver of protein evolution in prokaryotes.

The finding, published in PLoS Genetics, could change the way scientists study and model biological networks and protein evolution.

"Even at a meeting last summer, there were those that thought that bacteria genomes expanded mostly through duplications and others that argued that it was due to gene acquisition," wrote Howard Ochman, an evolutionary biologist at Yale University who was not involved in the research, in an Email to The Scientist. "Now we all have a paper to point to that does a very good job of answering this question," he said. "Their conclusions are really robust."

Prokaryotes, including bacteria and archaea, thrive in diverse conditions thanks to their ability to rapidly modify their repertoire of proteins. This is achieved in two ways: by receiving genes from other prokaryotes, called horizontal gene transfer -- the nefarious way that bacteria acquire antibiotic resistance -- or by gene duplication, in which an existing gene is copied, taking on a new or enhanced function as mutations accumulate.

Past analyses using few, distantly related genomes estimated that horizontal gene transfer contributes to, at best, 25 percent of the expansion of protein families -- that is, the addition of proteins with novel functions or structures. But the recent availability of numerous, closely related prokaryotic genomes tempted Todd Treangen and Eduardo Rocha at the Institut Pasteur in Paris to more accurately test which biological process is the main driver of prokaryote protein evolution. "The genomic data was finally there to do a more in depth study," said Treangen, now a postdoc at the University of Maryland.

The duo analyzed 110 genomes of varying size from 8 clades of prokaryotes, focusing in on 3,190 defined protein families. The results were unambiguous: 80 to 90 percent of protein families had expanded through horizontal gene transfer. In addition, the researchers found that the two processes have different evolutionary roles: transferred genes persist longer in populations while duplicated genes are transient but more highly expressed.

"Overall, the role of gene transfer in protein diversification has been underestimated," said Treangen. Still, he noted, they analyzed only a tiny fraction of the microbes that exist in the world, and further research should be done as more genomes become available.

It would be nice to study the same two processes in eukaryotes, said Patrick Keeling, a molecular evolutionary biologist at the University of British Columbia who was not involved in the research. Yet despite numerous documented cases of horizontal gene transfer in eukaryotes, including plants, it would be hard to test because of the lack of genomic data from enough closely related eukaryotes (which have significantly larger, less manageable genomes than prokaryotes).

Still, "it raises some really fascinating questions about whether [eukaryotes] evolve in the same way," said Keeling.

Treangen, T.J. et al., "Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes," PLoS Genetics, 7:e1101284, 2011.

The Scientist