September 3rd, 2008
A new method to study origin of life
U.S. researchers at Penn State University have developed a new computational method to understand how life began on Earth about four billion years ago. According to the scientists, their method ‘has the potential to trace the evolutionary histories of proteins all the way back to either cells or viruses, thus settling the debate once and for all over which of these life forms came first.’ The method, which is based on the study of an ancient group of proteins called retroelements, produces a tree-like diagram, called a phylogenetic tree. One of the team leaders said that ‘it is within our grasp to determine whether viruses evolved from cells or vice-versa.’ Fascinating! But read more…
You can see above an example of such a phylogenetic tree — for the baobab. “The baobab tree represents one of the most ancient species of life on the planet. In our paper, we investigate ancient and highly divergent proteins, called retroelements, whose evolutionary histories hold keys to uncovering the origins of life. Our research demonstrates that phylogenetic profiles generated using the Gestalt Domain Detection Algorithm-Basic Local Alignment Tool (GDDA-BLAST) provide an independent method for estimating the evolutionary histories of retroelements.” (Credit: Randen Patterson and Damian van Rossum, Penn State) Here is a link to a larger version of this picture (3,386 x 3,543 pixels, 6.80 MB).
This method has been developed at the Eberly College of Science of Penn State by Randen Patterson, an assistant professor of biology, with the help of Damian van Rossum, another assistant professor, and several other researchers.
Now, let’s look at the basis of this new computational method. “The team is focusing on an ancient group of proteins, called retroelements, which comprise approximately 50 percent of the human genome by weight and are a crucial component in a number of diseases, including AIDS. “Retroelements are an ancient and highly diverse class of proteins; therefore, they provide a rigorous benchmark for us to test our approach. We are happy with the results we derived, even though our method is in an early stage,” said Patterson. The team plans to make the algorithms that they used in their method available to others as open-source software that is freely available on the Web.”
For more information, please read the full Penn State news release. But for more details in plain English, you should read “Way to reveal the genesis of all life devised,” an article by Roger Highfield, Science Editor for The Telegraph, UK (September 2, 2008). “Many experts believe that the first kinds of life depended on RNA, a more flexible kind of genetic material than the DNA that today carries genes for most life on Earth. Now an American team proposes that a study be carried out of proteins that viruses and other parasites use to pirate DNA, and convert it into RNA, to reveal details of the kind of RNA genetic machinery that must have been present in the first life, which is estimated to have emerged about four billion years ago. The team at The Pennsylvania State University, Penn State, focuses on proteins such as the enzyme reverse transcriptase, which is used by the Aids virus (written in RNA) to alter the DNA or genetic material of an infected cell to produce more virus particles.”
This research work has been published online before print on September 2, 2008 by the journal Proceedings of the National Academy of Sciences as an open access article under the title “Phylogenetic profiles reveal evolutionary relationships within the ‘twilight zone’ of sequence similarity.” Here are two links to the abstract and to the full paper (PDF format, 6 pages, 475 KB).
For your convenience, here is an excerpt from the introduction of this highly technical article. “Here, we show that phylogenetic profiles generated with the Gestalt Domain Detection Algorithm–Basic Local Alignment Tool (GDDA-BLAST) are capable of deriving, ab initio, phylogenetic relationships for highly divergent proteins in a quantifiable and robust manner. Notably, the results from our computational case study of the highly divergent family of retroelements accord with previous estimates of their evolutionary relationships.”
When will we know if this new method is successful? Time will tell.
Sources: Penn State University Live News, September 2, 2008; and various websites
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