A new twist in the ‘Tree of Life’

Johann Peter Gogarten (left), and Kenneth Noll

Kenneth M. Noll and J. Peter Gogarten, professors of molecular and cell biology, and nine other scientists are publishing new findings in the March 16-20 Proceedings of the National Academy of Sciences (PNAS) about horizontal gene transfer in Thermotogales, heat-loving bacteria that are a research specialty of Noll, the lead author.

Gogarten, a leading researcher in horizontal gene transfer, Noll, and their colleagues found that the Thermotogales seem to acquire at least two major groups of genes from other organisms – from Archaea, a class of microbes which were differentiated from the bacteria in 1977, and from another group of bacteria that thrives in high temperatures.

The horizontal acquisition of genes from Archaea was established in 1999 by a co-author on the current paper, Karen E. Nelson of The J. Craig Venter Institute in Maryland. But at that time, it was thought that Thermotogales got as many as a quarter of their genes directly from Archaea.

The new research analyzes five genomes, where the earlier paper examined one, and it uses more complex and sophisticated databases made possible by the extensive gene sequencing that has gone on since 1999. It shows that Archaea have contributed fewer genes to the Thermotogales – possibly around 10 percent. But it also shows that the Thermotogales also gained an even larger fraction of genes from other heat-loving bacteria in their environment.

The findings reinforce the idea that horizontal gene transfer (HGT), or passing genes directly from one organism to another, is part of the evolutionary development of life.

HGT is consistent with Darwinian ideas of natural selection and enriches the possibilities of how nature creates new species, Noll says.

In HGT, rather than random mutations of genes being passed from parent cell to offspring, genes move directly from one microbe to another, over evolutionary or shorter periods of time, giving rise to new organisms.

HGT is found in microbes, one-celled organisms that can take DNA directly into their cells, and sometimes in plants, but it is thought to be uncommon in more complex organisms.

The new research, says Gogarten, “is a beautiful illustration that evolution in the microbial world follows very different rules than what occurs in plants and animals.”

Researchers in Europe have been less than enthusiastic about the theory of horizontal gene transfer, Gogarten says, but it is an idea at the forefront of research in the U.S., where it is the subject of controversy among scientists.

Gogarten, who recently began work on a $2.5 million NSF grant to examine how microbes fit into the “Tree of Life,” the pattern of evolutionary descent, has studied HGT for some 20 years. His specialty is computational biology, and his research team on the NSF grant, including Noll, will systematically search for ancient and modern clues of microbes transferring genes horizontally.

Noll, who with Gogarten has worked on three consecutive NASA-funded grants, specializes in Thermotogales, which are found in such hotbeds as sediments heated by volcanoes, deep oil wells, and freshwater hot springs. The bacteria group is the “poster child” for horizontal gene transfer, he says. Few other organisms live in its hot habitats, making it easier to establish the sources of its genes.

One of the co-authors of the current paper recently found a new type of Thermotogale that grows at more moderate or low temperatures, such as the sediments of Chesapeake Bay. But in one of the paper's major findings, Noll says, the researchers learned that it appears that the ancestor of Thermotogales grew in high temperature environments.

This has implications for understanding what could have been the ancestor of all organisms, he says. It has been theorized that the first life on earth grew in extremely high temperatures, an environment in which Archaea and Thermotogales now thrive.

To hear a podcast of Kenneth Noll talking about the new paper and horizontal gene transfer, click here.

To read a pre-print edition of the paper, click here.

For more information on the NSF research: http://advance.uconn.edu/2008/081208/08120811.htm