Category Archives: Viruses

A chimeric fusion of RNA and DNA viruses.

The discovery of a new family of viruses leads to speculations on possible modes recombination between RNA and DNA viruses.

The virosphere can be divided into three major classes; viruses with DNA genomes, retroviruses that reverse-transcribe their RNA genome into DNA during their lifecycle, and RNA-only viruses that don’t require DNA intermediates to replicate. In fact, viruses use all sorts of different permutations of genetic material; double-stranded RNA, single-stranded RNA (either negative or positive strand), dsDNA and ssDNA. Viruses evolve notoriously quickly and lateral gene transfer between them is rampant. However, gene transfer has most commonly occurred between closely related viruses or between those with similar replication mechanisms. A recent paper has reported the discovery of a new family of viruses that appear to have arisen via lateral gene transfer between a (non-retroid) +ve single-stranded RNA virus and a ssDNA virus.

Diemer and Stedman discovered the new virus whilst investigating viral diversity in a geothermal lake in California. Boiling Springs Lake is an acidic, high temperature lake with a purely microbial ecosystem composed of archaea, bacteria, and some single cell eukaryotes. Using a metagenomics approach (ie. large-scale sequencing  of environmental DNA from a virus particle sized fraction), they discovered the strange juxtaposition of a capsid protein (CP) gene related to those from the ssRNA plant-infecting Tombusviridae, with a rolling-circle replicase (Rep) gene most similar to those from the circular ssDNA-containing Circoviridae. Using primers designed against CP they confirmed the genome sequence of this putative virus, finding that it consisted of a single-stranded circular DNA containing 4 ORFs. ORFs 3 and 4 are of unknown function and unrelated to known genes. The virus contains a stem loop structure upstream of the Rep gene similar to those that serve as replication origins in other Circoviruses. Thanks to the chimeric origin of the Rep and CP genes, the authors termed it RNA-DNA hybrid virus (RDHV). This term is slightly open to misinterpretation as it could suggest that both molecules are actually encoding its’ genome, but to be clear this is a circular ssDNA virus whose capsid protein is derived from ssRNA viruses.

Organisation of RDHV. Note that ORFs 3 and 4 are not equivalent to those of Tombusviruses, and RDHV is twice the size of other Circoviruses.

Scanning databases of environmental sequence, the researchers found three other instances of homologous CP and Rep sequences arranged in the same configuration, two from global ocean surveys and one from the Sargasso Sea. This shows that RDHV defines a new family of viruses that are common in marine environments and could be more widespread. As CP and Rep are still highly similar to their sibling genes, it appears that the LGT event underlying the evolution of this new family occurred quite recently.

How did recombination occur between a non-retrovirus ssRNA virus and a DNA virus? A number of genes derived from non-retroid RNA viruses have been found in eukaryotic genomes, so perhaps this type of exchange is not as strange or rare as it may seem. The most likely scenario involves the RNA gene being converted into DNA by reverse transcription, followed by DNA-DNA recombination. As reverse transcriptase is not encoded by either virus, it could have been supplied in trans by retrotransposons, group II introns, or retroviruses within a common host cell. This brings us to the problem of metagenomic studies; they have amazing power to identify novel viruses and organisms, but yield very little information on the biology of what is found. In this case of RDHV and it’s family we do not know what their hosts are, don’t know the morphology of the viruses, and don’t know about the functions of half it’s 4 gene genome. I’m not sure how quickly these questions will be answered. Nevertheless, this study shows that amazing diversity is still out there being found, and yields insight into mechanisms underlying virus evolution – possibly in the deep past as well as more recently.

Diemer, G., & Stedman, K. (2012). A novel virus genome discovered in an extreme environment suggests recombination between unrelated groups of RNA and DNA viruses Biology Direct, 7 (1) DOI: 10.1186/1745-6150-7-13

Virophages and the evolution of transposable elements

Fischer, M., & Suttle, C. (2011). A Virophage at the Origin of Large DNA Transposons Science, 332 (6026), 231-234 DOI: 10.1126/science.1199412

This paper reports the discovery and characterisation of a virophage, Mavirus, and postulates that it’s similarities with a family of transposable elements suggest a common evolutionary origin.

Mavirus (white arrows) in the virion factory of CroV (CroV viral particles white arrow head, black arrow - a potentially defective CroV capsid)

Mavirus is the second virophage so far discovered. Both it and the other, Sputnik, parasitize giant viruses that infect protists. There is some controversy as to whether these viruses should be classified as virophages or a new class of satellite viruses. Virophages are predicted to have no nuclear phase in their infection cycle, to replicate in the virion factory of the host virus and to be dependent on enzymes provided by the host virus rather than the host cell. Mavirus is associated with the Cafeteria roenbergensis virus (CroV) that infects the marine phagotrophic flagellate C. roenbergensis. Mavirus can’t replicate in the absence of CroV, and CroV production and host cell lysis was reduced when infected with Mavirus.

The Mavirus has a 19kb circular double stranded DNA genome that is predicted to contain 20 protein coding genes (fig 1).  Between each gene the researchers found promoters that are highly similar to the predicted late promoter motif in CroV, implying that Mavirus gene expression is activated by the transcription machinery of CroV. Only four Mavirus genes showed homology with those on Sputnik, the other known virophage (including those encoding the capsid protein and a DNA pumping ATPase).

Figure 1. Genome diagram of Mavirus. Genes conserved with MP TEs are in red. Genes sometimes found in MP TEs in blue.

More genetic homology is found between Mavirus and a class of DNA transposons: the self-synthesising Maverick or Polinton Transposable elements (MP TEs). MP TEs are between 9 and 22kb long and encode up to 20 proteins. A conserved subset of genes is found in all MP TEs including a retroviral integrase (rve-INT) (responsible for DNA integration), a protein primed DNA polymerase B (PolB), an ATPase similar to those responsible for packaging dsDNA in viruses, and a cysteine protease with adenoviral homologues. Genes for all four of these proteins were found in Mavirus as well as another three often encountered in MP TEs.

The best evidence for a close evolutionary relationship between Mavirus and MP TEs was the identification of a region of synteny between Mavirus and a genomic fragment from the slime mold Polysphondylium pallidum that contains a MP TE-like fragment (fig 2).

Fig 2. Comparison of gene organisation between Mavirus and a truncated MP TE from P. pallidum. homologous genes are the same colour and the syntenic region shown in green.

Another resemblance between MP TEs and Mavirus relates to genome structure. MP TEs have terminal inverted repeats of several hundred nucleotides, and highly conserved ends starting with 5′-AG and ending with CT-3′. Although the Mavirus genome is a circular molecule at one point it encodes a ~50bp inverted repeat with the potential to adopt a hairpin structure. The adenine at the top of this hairpin was designated position 1 of the genome. Cutting the Mavirus genome between nucleotides 19,063 and 1 would result in the same termini as MP TEs and inverted repeats.

All these parallels between MP TEs and Mavirus suggest that the two are derived from a common ancestor. The question is whether the common ancestor was a transposable element or a virophage? The authors consider that the more parsimonious explanation is that a Mavirus ancestor (MVA) gave rise to MP TEs, and go on to suggest a possible evolutionary scenario. In early eukaryotic cells susceptible to infection by large DNA viruses there would be selective pressure on the host cells to stabilise relationships with a MVA. The acquisition of a retroviral integrase gene by MVA and integration in the host cell genome could have conferred protection against the large DNA virus. Various endogenisation of virophage events would create provirophages that may have led to various MP TEs. The close relationship between retroviruses and retrotransposons has long been known. This characterisation of the links between a DNA virus and a class of DNA transposable element yields similar insight into the evolution of mobile DNA and it’s importance in genomic evolution.