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A Plasmid Goes Viral

Credit: photo5963_fotolia/Adobe

Credit: photo5963_fotolia/Adobe

By Rick Cavicchioli & Susanne Erdmann

No one really knows how viruses evolved, but scientists looking for Antarctic viruses from extremely cold and salty lakes have discovered new clues.

Antarctica is probably the Earth’s most important continent for influencing global climate and ocean ecosystem function. Winds descending off the continent cool the surrounding seawater, causing an annual formation of sea-ice stretching up to 20 million km2 (about 2½ times the area of Australia). The cooling has two effects: it causes seawater to become more dense, and salt precipitates from the sea-ice as it forms, so the sea-ice essentially becomes fresh water. As a result, a downward force is generated that drives global ocean currents.

The cold Southern Ocean surrounding Antarctica also supports the growth of phototropic microbes that harvest the sun’s energy and fix CO2 from the atmosphere. These microbes, and others that recycle nutrients, represent the beginning of a marine food web that feeds krill and all other ocean life.

As one of the tiniest forms of microbes, viruses play essential roles in all of the Earth’s ecosystems. Viruses may cause about 20% of the cellular microbes in oceans to lyse and die each day, causing nutrient turnover and further microbial growth (http://tinyurl.com/abmjhtf). Viruses play particularly important roles in the Antarctic because its waters harbour fewer larger predators, so viruses can contribute even more to the natural turnover in these ecosystems (http://tinyurl.com/jvc5xl3).

DNA sequencing of entire Antarctic microbial communities in a freshwater lake on the Antarctic Peninsula discovered a high level of unique viruses (http://tinyurl.com/ybw8fuc3). The 2009 report in Science noted how the viral communities were dynamic, changing in response to the state of the ice cover on Lake Limnopolar.

In 2011 Cavicchioli’s laboratory at UNSW discovered a form of virus called a “virophage” at Organic Lake, a marine-derived hypersaline lake near Australia’s Davis Station in Antarctica (http://tinyurl.com/y79ng77a). Virophages depend on the coinfection of their host by another virus, typically a giant virus. While virophages negatively impact these larger viruses, Cavicchioli’s lab concluded that the interactions between the Organic Lake virophage and the larger virus could improve the ability of their algal host to photosynthesise, and hence contribute to a better functioning ecosystem.

Plasmids, Viruses and Promiscuity

In a twist on what biology can offer up from the Antarctic, we recently led a study that discovered a plasmid masquerading as a virus (http://tinyurl.com/yalyzus3). Plasmids are small, circular, double-stranded DNA molecules found in many types of micro­organisms. The findings, published in Nature Microbiology, mean there are new ways to consider how viruses have evolved.

The backdrop to the discovery was a 2013 study that analysed the genetic make-up of a microbial community in Deep Lake, a marine-derived system that has a salinity about ten times that of seawater and is the coldest aquatic environment known to support life – temperatures in the lake are as low as –20°C. The Cavicchioli group reported that the lake supported a community of very promiscuous microbes that exchanged DNA with each other (http://tinyurl.com/y8cpkya3). The haloarchaea microbes require very high levels of salt to grow, and can be found in environments like the Dead Sea in Israel and Lake Tyrrell in Australia, on salty fish, and in solar salterns worldwide where they colour the ponds pink/purple.

Another study of Deep Lake published in The ISME Journal by Cavicchioli’s group analysed proteins from environmental samples rather than DNA. It concluded that viruses were likely to be important in transferring DNA between the different types of haloarchaea (http://tinyurl.com/y89s7kdq).

A Plasmid Masquerading as a Virus

To advance our understanding about the haloarchaea and their viruses, Cavicchioli’s group took water samples from hypersaline lakes, including some from lakes in the Rauer Islands about 30 km away from Davis Station, and brought them back to the lab at UNSW. Erdmann isolated viruses from the water samples and sequenced their DNA so she could discover which types of viruses were present.

During this phase of the research she discovered that one of the sequences was for a plasmid, not a virus. The plasmids encoded proteins that were a part of virus-like particles. Furthermore, the particles harbouring the plasmids could be used to “infect” other haloarchaea that did not already contain the plasmid.

One of the fundamental distinctions between plasmids and viruses is that only viruses are known to encode proteins that go into viral DNA particles, and are capable of infecting cells. Plasmids, on the other hand, do not build particles that transfer by an active infection process. Instead, they move between cells, either when cells come together and transfer plasmid DNA during cell-cell contact or when naked extracellular plasmid DNA (e.g. arising from cell lysis) is taken up into new cells.

Thus the discovery blurs the boundaries between the definition of plasmids and viruses, with this new plasmid being able to infect – just like a virus.

Membrane Vesicles and Gene Exchange

Erdmann showed that the particles that the plasmid was packaged in was a “membrane vesicle” – a section of the host membrane that forms a “bleb” and detaches. Many life forms produce membrane vesicles. For instance, human cells use vesicles to move lipids and other cellular components around between cellular organelles. Some human viruses, like influenza and hepatitis C, require vesicles to propagate. Some of the vesicles have surface structures composed of proteins that have similarities to some of the plasmid proteins.

So what we have found is a new type of plasmid that behaves like a virus. Furthermore, the vesicles harbouring the plasmid appear to have structural features in common with vesicles in humans that play roles in both cell function and the life cycle of human viruses. These are interesting evolutionary connections.

Erdmann discovered different forms of the plasmid in halo­archaea from Deep Lake and the Rauer Island lakes. She learned that the plasmid could integrate into the DNA of host cells, excise from the host carrying long stretches of host DNA, get packaged into particles and then transfer to new hosts.

The discovery that the plasmid could transfer host DNA was another important finding as it demonstrated a plausible mechanism for the observed promiscuous gene exchange in Deep Lake. It will take more work to determine if the plasmid does perform this role in the lake, but there is certainly a good reason to go looking.

The Evolution of Viruses

Scientists studying viruses have wide-ranging opinions about how they evolved, including whether they pre-dated cells or evolved from cells. One theory, the escape hypothesis, is that viruses evolved as fragments of cellular DNA capable of infecting other cells so they could escape and propagate in a wider range of hosts. Our discovery of a virus-like plasmid fits with this theory while challenging how scientists think about the distinction between viruses and plasmids.

We speculate that plasmids that form plasmid vesicles may have been the predecessor of some viruses. Our reasoning is along the following lines.

It is now known that plasmids can produce proteins that go into host membranes, leading to the formation of specific types of membrane vesicles that harbour the plasmid. These plasmid vesicles then leave the host and go off to infect other hosts that do not already contain the plasmid. This phenomenon is like a virus.

Some viruses, called pleolipoviruses, reproduce by encapsulating themselves in vesicles made from lipids from the host membrane combined with their own proteins. Other viruses, such as head-tailed viruses, encode specific proteins that form heads, specific proteins that form tails, and other “machinery” that collectively makes these types of viruses structurally sophisticated entities.

The plasmid vesicles are less defined in their structure than many types of known viruses, perhaps being most similar to pleolipoviruses. It’s therefore conceivable that some types of viruses acquired their refined traits through an evolutionary process that commenced with plasmids that form plasmid vesicles.

Since ~80% of life on Earth lives at temperatures below 5°C, this research in Antarctica provides insights of global relevance. The discoveries also help to illustrate why Antarctica needs protection so that future generations can continue to learn and benefit for years to come.


Rick Cavicchioli is Professor of Biotechnology and Biomolecular Sciences at UNSW Sydney, where Susanne Erdmann is a Research Associate.