A DNA virus with the capsid of an RNA virus

19 July 2012

Boiling Springs Lake Lassen NPViral 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.

  • Virusstalker1

    I couldn’t find the 454 raw sequence data in the paper. Any author who creates HTS datasets should be depositing the raw data in databases such as SRA.

  • http://web.pdx.edu/~kstedman Kstedman

    The metagenomic sequence data were generated by the Broad Institute as part of the Moore Foundation Marine Microbiology Initiative and should be available at both CAMERA and NCBI, not sure about the “traces”, we never saw them.  I guess we did not make that clear in the manuscript. I’ll check to make sure that the sequence data are available.  -Ken Stedman

  • Kstedman

    Accession numbers SRX042554 and SRX042515 in SRA. 

  • http://www.facebook.com/profile.php?id=19714126 Josh Powell

    These guys are on to something big….they are from my home state of Oregon…I read this paper three times and at first said “Bullshi*t”  I even e-mailed the authors and had some nice chats with them.  There is still some work to be done. If you look at the paper there are some more experimental gaps (electron micrographs, purification, etc.) that need to addressed. They had great bioinformatics work from Koonin, but additional molecular biology is needed.

    With that being said, as my committee member Valerian Dolja, an expert on virus evolution told me…..there are always exceptions to the rule, you just have to look in enough places and you will find things you never expected.

  • gsgs
  • gsgs

    not wanting to read the whole paper, I found useful the summary from Krupovic on page 10.
    ( I’m mainly analysing sequences and I don’t know much about viruses anatomy
    and functionality except maybe influenza.)
    I’d like to have the 3 nucleotide sequences in my computer for analysis.
    Not so easy to figure out how to do this. I never heard about that GOS database.

  • tbontb

    I was told repeatedly that viruses have DNA or RNA as their genome, but never both. I guess this definition will now change. 

  • Prabhumeghanath66

    Is it that the virus is having both DNA and RNA as the genetic material?? or is it possible that after the DNA have been converted to RNA and there is mutation during protein assembly and because of this the Capsid looks as if it has coded from the RNA as found in that of RNA viruses??

  • http://www.virology.ws profvrr

    The viral genome is DNA, not both DNA and RNA. The idea is that the RNA virus sequences encoding the capsid protein was converted to DNA, which then recombined with the viral DNA genome.

  • http://www.virology.ws profvrr

    The genome of this recombinant virus is DNA, n0t DNA and RNA. The gene encoding the viral capsid was acquired from an RNA virus, but as a DNA copy.

  • Kstedman

    Sorry for any confusion, the virus genome that we found is clearly a DNA genome but somehow it picked up a gene from an RNA virus.  How that happened is the real (and extremely exciting) puzzle.

  • Bio2shameer

    Its a reverse transcription process from RNA viral Capsid  and form a cDNA . According to my knowledge if both codes same protein, then cDNA is arrived from the RNA viral Capsid . Otherwise  need to study the life cycle of that viruses     

  • rob

    Does the capsid protein bind directly to the genomic DNA, or is there a  matrix/tegument to enable packaging ? Are circovirus packaging signals similar to tombusvirus ones? Does it just package any DNA or RNA that’s around?

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