virology blog
About viruses and viral disease
On episode #342 of the science show This Week in Virology, the TWiVniks discuss the structure of a virus that reproduces in an extreme environment, long-term consequences of Ebolavirus infection, and VirScan, a method to identify the different virus infections you have had in your lifetime.
You can find TWiV #342 at www.microbe.tv/twiv.
Many microbes live in extreme environments, encountering conditions that are very hot, very cold, highly acidic, or very salty. The viruses that infect such microbes must also be able to retain infectivity in extreme conditions. How do they do it?
Clues come from the observations that the genomes of viruses that infect Archaea in extreme geothermal environments encode proteins that have never been seen before. The idea is that such unusual proteins must endow these viruses with the ability to maintain infectivity under extreme conditions.
The hosts of Rudiviruses (rudi=small rod in Latin), the Archea Sulfobolus islandicus, live at high temperatures (80° C) and low pH (3.0). These non-enveloped viruses consist of double-stranded DNA wrapped in a helical manner with thousands of copies of a 134 amino acid protein (illustrated; image credit). The three-dimensional structure of Sulfobolus islandicus rod-shaped virus 2 (SIRV2) reveals a new type of organization of virus particles, and provides clues about how it retains infectivity in extreme environments.
Resolution of the SIRV2 structure reveals that it consists of dimers of a single protein which forms helices that are tightly wrapped around the DNA genome. The result is a coiled DNA protected by a coat of protein that stabilizes and protects the genome. Without DNA, over half of the capsid protein is unstructured. Only in the presence of DNA does the viral protein form an alpha helix that wraps around the nucleic acid.
The DNA genome of SIRV2 is in the A-form, in contrast to B-form DNA which is found in most other organisms. The two types of DNA differ in their geometry and dimensions. It was previously thought that A-DNA occurs only when the nucleic acid is dehydrated.
These two usual properties of SIRV2 are also found in gram positive bacteria which form desiccation and heat resistant spores when starved of nutrients. Sporulation is accompanied by a change in the bacterial genome from B-DNA to A-DNA, which is caused by the binding of small acid-soluble proteins. Like the SIRV2 capsid protein, small acid-soluble proteins of spore-forming bacteria are unstructured in solution, and become alpha helices when bound to DNA. These observations suggest that binding of the SIRV2 capsid protein changes the viral DNA to the A-form, conferring stability in extreme environments.
Viral genomes are unusual because they can be based on RNA or DNA, in contrast to all cellular life forms, which have DNA as their genetic information. An unusual new virus has been discovered that appears to have sequences from both an RNA and a DNA virus.
The new virus was identified during a study of viral diversity in an extreme environment, Boiling Spring Lake. You would never want to swim there: it is acidic (pH 2.5) and hot (52° − 95° C). But the lake is not devoid of living things: it is inhabited by various bacteria, Archaea, and unicellular eukaryotes. Where there is life, there are viruses, which leads us to an expedition to determine what kinds of viruses can be found in Boiling Spring Lake.
To answer this question, Goeff Diemer and Kenneth Stedman sequenced viral DNA extracted from purified viral particles from Boiling Spring Lake water. Their analyses revealed the presence of a virus with a circular, single-stranded DNA genome similar to that found in members of the Circoviridae (this virus family includes porcine circovirus and chicken anemia virus). What surprised the investigators was that the gene encoding the viral capsid protein was similar to that from viruses with single-stranded RNA genomes, including viruses that infect plants (Tombusviridae) or fungi. The authors call it ‘RNA-DNA hybrid virus’, or RDHV. The host of RDHV is unknown but could be one of the eukaryotes that inhabit Boiling Spring Lake.
RDHV probably arose when a circovirus acquired the capsid protein of an RNA virus by DNA recombination. This event likely occurred in a cell infected with both viruses. A cellular reverse transcriptase might have converted the circovirus RNA genome to DNA to allow recombination to occur. RDHV is unusual because genetic exchanges among viruses are restricted to those with similar genome types.
To determine if RDHV is an oddity, the authors searched the database of DNA sequences obtained from the Global Ocean Survey. They found three RDHV-like genomes, indicating that these viruses exist in the ocean. Whether they are present elsewhere is a question that should certainly be answered. It is important to determine whether recombination between RNA and DNA viruses is a common means of gene exchange, or whether it is a rarity.
The discovery of RDHV could have implications for viral evolution. It has been suggested that the first organisms that evolved on earth were based on RNA molecules with coding and catalytic capabilities. Later, DNA based life evolved, and today both DNA based and RNA based organisms co-exist. Viruses like RDHV could have emerged during the transition from an RNA to a DNA world, when a new DNA virus captured the gene encoding an RNA virus capsid. In other words, RNA genes that had already evolved were not discarded but appropriated by DNA viruses. This scenario would have required some mechanism for converting RNA into DNA (reverse transcriptases?). The finding of RDHV-like viruses in the ocean suggests that a common ancestor emerged some time ago which diversified into different environments. More RDHV-like viruses must be isolated and studied before we can determine whether or not these viruses are very old, and to deduce their implications for viral evolution.
Diemer GS, Stedman KM. 2012. A novel virus discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses. Biology Direct 7:13.