A Viral Closeup

Computer reconstruction of electron microscope images reveals surprising bends in viral DNA.

The phi29 bacteriophage is an efficient infection machine—it fires its genome into a host bacterium, hijacks the host’s cellular equipment, and assembles an army of new viruses for its next mission. For the first time, scientists have produced sub-nanometer resolution pictures of the virus, revealing some striking new details—including an unexpectedly tight twist of DNA suggestive of how the virus springs into action. The results appear in the June issue of Structure.


A 3D rendition of the phi29 bacteriophage particle reconstructed to 7.8 Angstrom resolution from cryo-electron micrographs reveals a tightly wound donut-shaped toroid of DNA (red section inside of dotted box) wedged in the tail of the phage.  Reprinted from Duda, RL, and Conway, JF, Asymmetric EM Reveals New Twists in Phage, Structure 16 (2008), with permission from Elsevier“We use structure as a way to try and understand how viruses function,” says Timothy Baker, PhD, professor of chemistry/biochemistry and molecular biology at the University of California, San Diego who led the collaboration between UCSD and the University of Minnesota. “The more we can learn from structure, the better we’ll understand the whole infection process and perhaps ways to circumvent it.”


Using computer reconstruction, Baker and his colleagues aligned roughly 12,000 electron microscope images of frozen viral particles at different angles and fused them into a 3-D picture of the assembled phage—including its head (either full of DNA or empty), its tail, and the head-tail connector. “You have to go through an iterative process of looking at all 12,000 images with respect to a model which is a cube of data that’s 900 pixels on a side. So the computational challenges are pretty severe,” Baker says. “This couldn’t have been done even a few years ago, not without really dedicated supercomputer power.”


The resolution achieved—8 Angstroms—was two-fold higher than ever before for an asymmetric virus (where researchers cannot exploit symmetry to reduce complexity). At this resolution, individual alpha helices (in the proteins that make up the head-tail connector piece of the virus) become distinguishable as tube-like structures. Baker’s team compared their picture of the viral head-tail connector with atomic-level models of this structure that were available from X-ray crystallography, and showed that the alpha helices matched up. “It helped us verify that what we were seeing in our map was in fact believable,” he says.


Their reconstruction revealed a surprise: the DNA in the tail of the phage bends into a tight coil—a toroid, or donut-like, shape. DNA isn’t expected to bend so tightly over short distances. “It turns out if you talk to people who know something about DNA, they say it is possible,” Baker says. “They just haven’t seen it in a biological system like this before.”


“In terms of shock value, that was amazing,” comments John E. Johnson, PhD, professor of molecular biology at The Scripps Research Institute who occasionally collaborates with Baker. The bacteriophage must pack its DNA into a tiny space against tremendous forces, and Johnson speculates that the toroid may act as a plug to hold the DNA inside until it’s ready to be injected into the host. “It’s so suggestive when you look at how this thing is wound up in this little cavity,” he says.


Prior to this work, Johnson’s team had published one of the highest resolution reconstructions of an asymmetric virus to date (17 Angstroms—as reported in Science in 2006). “We saw a lot of interesting things,” he says. “But this paper has pushed it to a higher level.”


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