Giant viruses should be included reconstructions of the tree of life, researchers report in a new study. The mimivirus, shown here (small black hexagons) infecting an amoeba, is as big as some bacterial cells and shares some ancient protein structures with most organisms. |
A
new study of giant viruses supports the idea that viruses are ancient
living organisms and not inanimate molecular remnants run amok, as some
scientists have argued. The study may reshape the universal family tree,
adding a fourth major branch to the three that most scientists agree
represent the fundamental domains of life.
The new findings appear in the journal BMC Evolutionary Biology.
The
researchers used a relatively new method to peer into the distant past.
Rather than comparing genetic sequences, which are unstable and change
rapidly over time, they looked for evidence of past events in the
three-dimensional, structural domains of proteins. These structural
motifs, called folds, are relatively stable molecular fossils that—like
the fossils of human or animal bones—offer clues to ancient evolutionary
events, said University of Illinois crop sciences and Institute for
Genomic Biology professor Gustavo Caetano-Anollés, who led the analysis.
“Just
like paleontologists, we look at the parts of the system and how they
change over time,” Caetano-Anollés said. Some protein folds appear only
in one group or in a subset of organisms, he said, while others are
common to all organisms studied so far.
“We
make a very basic assumption that structures that appear more often and
in more groups are the most ancient structures,” he said.
Most efforts to document the relatedness of all living things have left viruses out of the equation, Caetano-Anollés said.
“We’ve
always been looking at the Last Universal Common Ancestor by comparing
cells,” he said. “We never added viruses. So we put viruses in the mix
to see where these viruses came from.”
The
researchers conducted a census of all the protein folds occurring in
more than 1,000 organisms representing bacteria, viruses, the microbes
known as archaea, and all other living things. The researchers included
giant viruses because these viruses are large and complex, with genomes
that rival—and in some cases exceed—the genetic endowments of the
simplest bacteria, Caetano-Anollés said.
“The
giant viruses have incredible machinery that seems to be very similar
to the machinery that you have in a cell,” he said. “They have
complexity and we have to explain why.”
Part
of that complexity includes enzymes involved in translating the genetic
code into proteins, he said. Scientists were startled to find these
enzymes in viruses, since viruses lack all other known protein-building
machinery and must commandeer host proteins to do the work for them.
In
the new study, the researchers mapped evolutionary relationships
between the protein endowments of hundreds of organisms and used the
information to build a new universal tree of life that included viruses.
The resulting tree had four clearly differentiated branches, each
representing a distinct “supergroup.” The giant viruses formed the
fourth branch of the tree, alongside bacteria, archaea and eukarya
(plants, animals and all other organisms with nucleated cells).
The researchers discovered that many of the most ancient protein folds –
those found in most cellular organisms—were also present in the giant
viruses. This suggests that these viruses appeared quite early in
evolution, near the root of the tree of life, Caetano-Anollés said.
The
new analysis adds to the evidence that giant viruses were originally
much more complex than they are today and experienced a dramatic
reduction in their genomes over time, Caetano-Anollés said. This
reduction likely explains their eventual adoption of a parasitic
lifestyle, he said. He and his colleagues suggest that giant viruses are
more like their original ancestors than smaller viruses with pared down
genomes.
The researchers also found that viruses appear to be key “spreaders of information,” Caetano-Anollés said.
“The protein structures that other organisms share with viruses have a
particular quality, they are (more widely) distributed than other
structures,” he said. “Each and every one of these structures is an
incredible discovery in evolution. And viruses are distributing this
novelty,” he said.
Most
studies of giant viruses are “pointing in the same direction,”
Caetano-Anollés said. “And this study offers more evidence that viruses
are embedded in the fabric of life.”
The
research team included graduate student Arshan Nasir; and Kyung Mo Kim,
of the Korea Research Institute of Bioscience and Biotechnology.
