boiling spring lake

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.