Antarctic mystery microbe could tell us where viruses came from

The lake in Antarctica where the R1S1 strain of Halorubrum lacusprofundi was discovered

Alyce Hancock

Via newscientist.com by Michael Marshall

A peculiar Antarctic microbe may offer a clue to one of the biggest mysteries in evolution: the origin of viruses.

The microorganism is host to a fragment of DNA that can build a capsule around itself. It may help solve the mystery of how viruses first arose.

Viruses are not like other life forms. Arguably, they are not alive at all. All other living things are made of cells: squashy bags filled with the other essential molecules of life. Cells are intricate machines that can feed and reproduce independently.

Viruses are much simpler. A typical virus is a small piece of genetic material encased in a shell called a capsid. On its own, a virus can do little. But if it enters a living cell, it starts making copies of itself. Viruses often harm their hosts: for instance, the human immunodeficiency virus (HIV) can cause AIDS when it infects a person.

Biologists have puzzled for decades about where viruses come from. Are they an older, simpler form of life – or are they parasites that arose only once cells had evolved?

 
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Ricardo Cavicchioli of the University of New South Wales in Australia and his colleagues have found a microorganism in the lakes of the Rauer Islands off the coast of Antarctica that might shed some light on the question. The organism, which they named Halorubrum lacusprofundi R1S1, is an archaean: a kind of single-celled organism that looks like a bacterium, but actually belongs to a separate domain of life.

The group knew that viruses often play an important role in Antarctic ecosystems, so team member Susanne Erdmann searched for viruses inside the organism’s cells. She found something unexpected: a plasmid.

Plasmids are small fragments of DNA, often circular, that reside in living cells. They are not part of the cell’s main genome, and can replicate themselves independently. Often, a plasmid will carry a gene that is somehow useful to the cell: for instance, antibiotic resistance genes are sometimes found on plasmids.

The plasmid Erdmann found, which the team calls “pR1SE”, is unusual. The genes it carries allow it to make vesicles – essentially bubbles made of lipids – that enclose it in a protective layer. Encased in its protective bubble, pR1SE can leave its host cell to seek out new hosts.

In other words, pR1SE looks and acts a lot like a virus. But it carries genes that are found only on plasmids, and lacks any telltale virus genes. It is a plasmid with the attributes of a virus. “There really are no major distinctions left between plasmids and viruses,” says Cavicchioli.
 
Escaping genes

He suggests that viruses could have evolved from plasmids like pR1SE, by acquiring genes from their host that allowed them to make a hard capsid shell rather than a soft vesicle.

This lines up with existing evidence on the origin of viruses.

There have been three leading ideas: either viruses originated before cells, or some cells evolved simpler forms and became viruses, or genes “escaped” from cells and became viruses. This third escape hypothesis has gathered support in recent years: in March 2017, a study suggested that many capsid proteins can be traced back to proteins found in cells.

The evidence implies that such escapes began early in the history of life, says Patrick Forterre of the Pasteur Institute in Paris. “Traditionally the escape hypothesis has been associated with the idea that viruses are recent,” he says. “Now the escape hypothesis should be viewed in a broader context.” The first viruses may have escaped from some of the first cells on Earth.

Journal reference: Nature Microbiology, DOI: 10.1038/s41564-017-0009-2

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