Ever since I first discovered them as a student, sometime in 1976, I have found retroviruses fascinating. Not quite as fascinating as Ebola, possibly, but captivating nonetheless. The whole concept of a virus that converts a perfectly ordinary mRNA into dsDNA, then inserts it into the host chromosome as a provirus in a eukaryotic version of lysogeny – was truly wonderful.
And as the years have gone by, I have seen no reason to lessen the feeling of wonderment: other
viruses – now called pararetroviruses, including both hepadnaviruses and plant viruses – whose replication starts at a different position in the cycle have been found; these and retroviruses have been integrated into a whole family of “reverse transcribing elements” – retrons – which include prokaryote transposons; HIV burst in on the scene, and suddenly we know so much about how the immune system works, because a virus messes with it so well.
But the actual mechanics of one particular process have consistently escaped elucidation – until now. The 11 November issue of Nature contains, apart from only the second SF short-short story by a South African (kudos, Anand!), a Letter of great interest.
The mechanism of retroviral integration from X-ray structures of its key intermediates
Goedele N. Maertens, Stephen Hare & Peter Cherepanov
Nature 468,326–329 (11 November 2010) doi:10.1038/nature09517
To establish productive infection, a retrovirus must insert a DNA replica of its genome into host cell chromosomal DNA. This process is operated by the intasome, a nucleoprotein complex composed of an integrase tetramer (IN) assembled on the viral DNA ends. The intasome engages chromosomal DNA within a target capture complex to carry out strand transfer, irreversibly joining the viral and cellular DNA molecules. Although several intasome/transpososome structures from the DDE(D) recombinase superfamily have been reported, the mechanics of target DNA capture and strand transfer by these enzymes remained unclear. Here we report crystal structures of the intasome from prototype foamy virus in complex with target DNA, elucidating the pre-integration target DNA capture and post-catalytic strand transfer intermediates of the retroviral integration process. [my emphasis – Ed] The cleft between IN dimers within the intasome accommodates chromosomal DNA in a severely bent conformation, allowing widely spaced IN active sites to access the scissile phosphodiester bonds. Our results resolve the structural basis for retroviral DNA integration and provide a framework for the design of INs with altered target sequences.
Basically, these folk have managed to freeze-frame several different stages of the process in crystals, by clever use of synthetic DNA targets – and then solved the structures. NOT trivial, and the pictures are absolutely superb. So are the movies…but you need to subscribe to Nature to see those.
Harking back to a previous post – Entrance, Entertainment and Exit, anyone? – the more we know about viruses, the more we can mess with them. And this is a VERY good step along that road.