Study of Giant Viruses Shakes Up Tree of Life

[Pappa]

Study of Giant Viruses Shakes Up Tree of Life

ScienceDaily (Sep. 13, 2012) — 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.

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[cowiz]

Ag a do do do push pineapple shake the tree

[PsychoSerenity]

[orpheus]

Very interesting finding.

On a humorous note, it reminds me of Giant Microbes. Like teddy bears, but...different...

Check out the animations toward the bottom of these pages:

Black Death

and Flesh Eating bacteria

[Audley Strange]

What an excellent tale. I'll be looking forward to this. We're such clever organic compounds.

[Calilasseia]

The paper is here, viz:

Giant Viruses Coexisted With The Cellular Ancestors And Represent A Distinct Supergroup Along With The Superkingdoms Archaea, Bacteria And Eukarya by Arshan Nasir, Kyung Mo Kim and Gustavo Caetano-Anolles, BMC Evolutionary Biology, 12(1): 156 (24th August 2012)

Abstract

Background

The discovery of giant viruses with genome and physical size comparable to cellular organisms, remnants of protein translation machinery and virus-specific parasites (virophages) have raised intriguing questions about their origin. Evidence advocates for their inclusion into global phylogenomic studies and their consideration as a distinct and ancient form of life.

Results

Here we reconstruct phylogenies describing the evolution of proteomes and protein domain structures of cellular organisms and double-stranded DNA viruses with medium-to-very-large proteomes (giant viruses). Trees of proteomes define viruses as a ‘fourth supergroup’ along with superkingdoms Archaea, Bacteria, and Eukarya. Trees of domains indicate they have evolved via massive and primordial reductive evolutionary processes. The distribution of domain structures suggests giant viruses harbor a significant number of protein domains including those with no cellular representation. The genomic and structural diversity embedded in the viral proteomes is comparable to the cellular proteomes of organisms with parasitic lifestyles. Since viral domains are widespread among cellular species, we propose that viruses mediate gene transfer between cells and crucially enhance biodiversity.

Conclusions

Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet’s biosphere.

[Pappa]

Who was it who wrote about a hypothetical life form that may have acted as a scaffold for our original ancestor? This report reminded me of that.

[Blind groper]

I have always believed viruses are living things. The major characteristics of life are three fold (at least until we find suitably alien extraterrestrials)

1. Based on carbon chemistry
2. Able to reproduce
3. Able to evolve.

Viruses most clearly share those three qualities. It is good to see some recognition of their status as 'life'.

[Horwood Beer-Master]

The paper is here, viz:

Giant Viruses Coexisted With The Cellular Ancestors And Represent A Distinct Supergroup Along With The Superkingdoms Archaea, Bacteria And Eukarya by Arshan Nasir, Kyung Mo Kim and Gustavo Caetano-Anolles, BMC Evolutionary Biology, 12(1): 156 (24th August 2012)

...Conclusions

Results call for a change in the way viruses are perceived. They likely represent a distinct form of life that either predated or coexisted with the last universal common ancestor (LUCA) and constitute a very crucial part of our planet’s biosphere.

Isn't the wording of that conclusion a bit contradictory? I mean if viruses are indeed a distinct branch of the tree of life, and existed alongside (or predated) the last universal common ancestor; then the last universal common ancestor is not in fact the last universal common ancestor; something earlier must have been instead (unless anyone wants to propose a separate abiogenesis event for viruses).


Nitpicking I know (since it's clear what they mean), but it kind of jumped out at me as I read it.

[JimC]

Who was it who wrote about a hypothetical life form that may have acted as a scaffold for our original ancestor? This report reminded me of that.

Was it the guy who thought compounds in clay may have done the job of being a scaffold?

Some sort of hyphenated name, I recall...

[Horwood Beer-Master]

Who was it who wrote about a hypothetical life form that may have acted as a scaffold for our original ancestor? This report reminded me of that.

Was it the guy who thought compounds in clay may have done the job of being a scaffold?

Some sort of hyphenated name, I recall...

But it's pronounced "Throat Warbler Mangrove"...

[Bella Fortuna]

Very interesting finding.

On a humorous note, it reminds me of Giant Microbes. Like teddy bears, but...different...

Check out the animations toward the bottom of these pages:

Black Death

and Flesh Eating bacteria

My son has a collection of those.

[klr]

Very interesting finding.

On a humorous note, it reminds me of Giant Microbes. Like teddy bears, but...different...

Check out the animations toward the bottom of these pages:

Black Death

and Flesh Eating bacteria

My son has a collection of those.

[rasetsu]

Who was it who wrote about a hypothetical life form that may have acted as a scaffold for our original ancestor? This report reminded me of that.

Was it the guy who thought compounds in clay may have done the job of being a scaffold?

Some sort of hyphenated name, I recall...

Graham Cairns-Smith

His hypothesis is discussed in The Blind Watchmaker, Ch. 6. (Dawkins alludes to another precursor theory supposedly in Dawkins' earlier writing. I know not.)

[JimC]

Who was it who wrote about a hypothetical life form that may have acted as a scaffold for our original ancestor? This report reminded me of that.

Was it the guy who thought compounds in clay may have done the job of being a scaffold?

Some sort of hyphenated name, I recall...

Graham Cairns-Smith

His hypothesis is discussed in The Blind Watchmaker, Ch. 6.

Thanks, rasetsu, that's the bloke I was thinking of...