Integration of arenavirus DNA into the cell genome

Is that title correct? Arenaviruses have an RNA genome which is not known to be copied into DNA at any stage of the replication cycle. How could a DNA copy of this virus be produced and be inserted into the host genome?

The RNA genome of retroviruses is converted to a DNA form during viral replication by the viral enzyme reverse transcriptase. The viral DNA then integrates into the host’s genome, becoming a permanent part of the cell. These events have no counterparts during replication of arenaviruses. The RNA genomes of these viruses are copied via an RNA intermediate, entirely in the cytoplasm of the cell. Nevertheless, the authors of a recent study found a DNA copy of the RNA genome of lymphocytic choriomeningitis virus (LCMV), a commonly studied arenavirus, integrated into host cell DNA.

This unusual story began in 1979 with the report that DNA complementary to the RNA genome of LCMV can be detected in about 1 in 10³ to 10⁴ infected cells. The authors speculated that retroviruses were involved but did not provide mechanistic evidence. Eighteen years later, the authors subcloned these cells to produce cell lines containing LCMV DNA. They then used polymerase chain reaction to isolate LCMV DNA from the cloned cells, including the cellular sequence flanking the viral genome. Nucleotide sequence analysis revealed that both cell lines contain a copy of the viral glycoprotein (GP) gene joined to cellular sequences encoding an IAP (intracisternal A type) retrotransposon. The authors identified LCMV integration both in cultured cells and infected mice.

Retrotransposons are sequences related to retroviruses that are found in the genome of many organisms. The gene content and arrangement are similar to retroviruses, but they lack an extracellular phase: they do not encode an env gene. Retrotransposons may be retroviral progenitors, or degenerate forms of these viruses. They are amazingly abundant: 42% of the human genome is made up of retrotransposons.

Based on their experimental results, the authors proposed that the following events occurred in a cell infected with LCVM. During copying of the retrotransposon RNA into a cDNA copy by reverse transcriptase, the enzyme switched templates and began copying the LCMV GP RNA. This hybrid DNA – retrotransposon linked to LCVM sequences –  then integrated into the host genome.

The results reported in this paper have enormous implications for evolution and for human gene therapy. Because retrotransposons transpose most efficiently in the thymus and testicles, the recombination events described could lead to transmission of RNA virus genes in the germline. Therefore the contribution of non-retroviral RNA viruses to evolution of the mammalian genome might be greater than previously believed. In addition, it is possible that RNA virus vectors used for gene therapy could integrate into the human genome via the mechanism described in this study. Such integration could lead to undesired mutation such as activation of oncogenes. Therefore the ability of specific RNA virus vectors to integrate into the human genome should be carefully tested before the vectors are approved for use in humans.

Rolf M. Zinkernagel, Paul Klenerman, Hans Hengartner (1997). A non-retroviral RNA virus persists in DNA form Nature, 390 (6657), 298-301 DOI: 10.1038/36876

M. B. Geuking, J. Weber, M. Dewannieux, E. Gorelik, T. Heidmann, H. Hengartner, R. M. Zinkernagel, L. Hangartner (2009). Recombination of Retrotransposon and Exogenous RNA Virus Results in Nonretroviral cDNA Integration Science, 323 (5912), 393-396 DOI: 10.1126/science.1167375