Friday, 3 July 2015

Molecule(s) of the Month July 2015: Protecting DNA in a hot bath of acid!

Image result for RudivirusesThe recent determination of the structure of the bacteriophage Sulfobolus islandicus rod-shaped virus 2 (SIRV2) caught my eye for a number of reasons. As you can see (above),  the virus gets its name from the Latin for a short rod. It infects thermophilic archaebacteria that live at around 80° C at low pH (hence the acid bath!). The genome is packed into the middle through a few thousand small proteins (the green globules left). Not too dissimilar to M13 phage, you might say, or Tobacco Mosaic Virus? Both stalwarts of Molecular Biology over the last 50 years. Well for a start, M13 packages its genome as a single stranded circle of DNA, while TMV has an RNA genome. So how did SIRV2 make it to the hallowed pages of Science Journal. It would appear to be all in a letter! 

Image result for Xray double helix franklin
If you cast your mind back to the heady days of the early 1950s, when structural biologists had the challenging task of interpreting X-ray data from proteins and nucleic acids in the absence of extensive, online structural data bases. You may recall the debate over the three dimensional organisation of the two strands of polynucleotides that make up DNA. Was it the A form or the B form? The data were better for A form crystalline material, which led Rosalind Franklin to focus on that particular data set. The B form (both forms differ in respect of solvation) on the other hand provided Watson and Crick with the information needed to propose the now famous DNA double helix. So ever since then, molecular biologists have always viewed non-B form DNA with a healthy level of scepticism. I wont expand on it here, but we now know that DNA takes many more structural excursions as it goes about its business. DNA can adopt a Z form, can form quadruplexes, can exhibit functional kinking and bending and can even form cross over structures during recombination. Not forgetting my own personal favourite, the flipped out base.

Fig. 3Getting back to SIRV2, the genome is packaged into the A form and interestingly, the DNA provides the stabilisation energy needed to convert the protein subunits from partially unfolded to rock solid scaffolding and insulation. (One of my NMR colleagues, Jon Waltho and I published on this phenomenon many years ago: I think it was one the first papers to provide evidence for this process in a DNA binding protein?). Just think of the transition from water to ice: that's what happens when protein and DNA meet. The authors of this work on SIRV2, propose that the combination of the protein structure and the A form of the DNA gives rise to a level of protection akin to that found in bacterial spores. Hence, a protein can provide protection for the genome under extreme conditions. (As an aside, I was stunned to find out yesterday that the pupae of Tsetse flies can withstand boiling bleach! I wonder what their coat proteins look like!). In the diagrams, A-D, above, the interactions between the proteins and the DNA is shown from different positions. Finally in D, you can see the higher order arrangement of the A-form super-helix in the virus particle. Normally, I show images from X-ray crystallography, but this work from Di Maio and colleagues has been carried out using the relatively new and rapidly expanding field of cryo-electron microscopy, adding a new dimension to acids and bases!

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