News: Transfer RNA transforms tree of life
- From: "Robert Karl Stonjek" <rstonjek@xxxxxxxxxxxxxx>
- Date: Sat, 8 Mar 2008 20:12:45 -0500 (EST)
Transfer RNA transforms tree of life
Posted by Elie Dolgin
[Entry posted at 7th March 2008 01:25 PM GMT]
A comparison of transfer RNAs has revealed the roots of the tree of
life, indicating ancient origins for Archaea and viruses, according to
research published yesterday in PLoS Computational Biology.
Since the discovery that ribosomal RNA can reveal evolutionary
relationships between organisms, researchers have split the universal tree
of life into three main branches: the superkingdoms Archaea, Bacteria, and
Eukarya. But the root of the tree has remained controversial. Also, this
tripartite tree of "life" has omitted viruses, which have long been
considered as "not living." To resolve the timeline of diversification and
the origin of viruses, therefore, a new molecular marker was needed.
Enter tRNA. "Transfer RNAs are ancient molecules," said Gustavo
Caetano-Anollés of the University of Illinois at Urbana-Champaign. "They're
molecular fossils." Caetano-Anollés and his colleague Feng-Jie Sun
investigated the sequence and structure of hundreds of tRNAs to probe for
deep evolutionary relationships in the tree of life. When they tried
standard phylogenetic methods, however, no clear patterns emerged. So they
grouped together tRNAs from the same superkingdoms and from viruses,
assuming that the different taxa must have evolved independently, and looked
for trees that required the fewest evolutionary steps. "We bombarded the
system with alternative hypotheses and chose the ones that fit the data
best," Caetano-Anollés told The Scientist. Consistently, the trees with the
fewest steps showed Archaea as most ancient, followed by viruses, Eukarya,
and Bacteria. And viruses were not only very old; they were also tightly
linked to Archaea.
Russell Doolittle of the University of California at San Diego, who
was not involved with the work, called the results "provocative." But he
cautioned that the analysis might be prone to a tree reconstruction artifact
known as "long branch attraction," where rapidly evolving lineages seem to
be closely related regardless of their true evolutionary relationships.
Doolittle also told The Scientist that he was "surprised there were enough
virus tRNAs to do this." Caetano-Anollés conceded that only around 20 viral
tRNAs were included, but he argued that the results are robust because the
viral tRNAs clustered together even when he divided viruses infecting
Eukarya or Bacteria into separate groups.
So, does the tRNA-derived phylogeny match the true tree of life? Last
year, Caetano-Anollés also published a paper in Genome Research that
supports the ancient origin of Archaea based on proteome architecture,
although that study did not consider viruses. Whether the timeline of these
molecules matches the timeline of organismal diversification, however,
remains to be seen. "You could take different molecules and get a different
topology," says Caetano-Anollés. "But tRNA is so old that it might represent
very ancient relationships, such as the rooting of the tree of life."
Source: TheScientist
http://www.the-scientist.com/blog/display/54410/
Posted by
Robert Karl Stonjek
.
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