A Lean, Mean DNA Packaging Machine – NIH Director's Blog

A Lean, Mean DNA Packaging Machine – NIH Director's Blog

A Lean, Mean DNA Packaging Machine

Posted on June 7th, 2018 by Dr. Francis Collins

Credit: Victor Padilla-Sanchez, The Catholic University of America, Washington, D.C.

All plants and animals are susceptible to viral infections. But did you know that’s also true for bacteria? They get nailed by viruses called bacteriophages, and there are thousands of them in nature including this one that resembles a lunar lander: bacteriophage T4 (left panel). It’s a popular model organism that researchers have studied for nearly a century, helping them over the years to learn more about biochemistry, genetics, and molecular biology [1].

The bacteriophage T4 infects the bacterium Escherichia coli, which normally inhabits the gastrointestinal tract of humans. T4’s invasion starts by touching down on the bacterial cell wall and injecting viral DNA through its tube-like tail (purple) into the cell. A DNA “packaging machine” (middle and right panels) between the bacteriophage’s “head” and “tail” (green, yellow, blue spikes) keeps the double-stranded DNA (middle panel, red) at the ready. All the vivid colors you see in the images help to distinguish between the various proteins or protein subunits that make up the intricate structure of the bacteriophage and its DNA packaging machine.

Victor Padilla-Sanchez, formerly a postdoc in Venigalla Rao’s lab at The Catholic University of America, Washington, D.C., created these wonderfully detailed images. He did it by overlaying publicly available structural data for all the proteins that make up the bacteriophage T4 onto an electron micrograph image of the bacteriophage.

Then, using specialized Chimera Visualization Software on a high-performance computer, Padilla-Sanchez assembled each and every one of the bacteriophage’s approximately 2,000 proteins into this virtual 3D model. It was tedious arranging each individual protein’s crystal structure to get them to fit together just right all the way down to the atomic level. Padilla-Sanchez says it only became possible to put the final pieces together in 2015, when a team including Rao and Padilla-Sanchez solved the structure for the last of the proteins [2].

The Rao Lab wants to understand exactly how the virus and its packaging machine work and are assembled. The hope is that the bacteriophage T4 might one day be re-engineered and put to use in new treatments or vaccines for a range of health conditions, including cancer and hard-to-treat infections such as HIV.

The Rao lab already has evidence suggesting it’s possible to engineer the bacteriophage to deliver a specific antigen directly to cells of the immune system. They also envision delivering DNA encoding a toxic compound directly to cancer cells. This carefully constructed series of images, a winner in the Federation of American Societies for Experimental Biology’s 2017 BioArt competition, will be essential for that kind of future viral engineering.

References:

[1] Bacteriophage T4 genome. Miller ES, Kutter E, Mosig G, Arisaka F, Kunisawa T, Rüger W. Microbiol Mol Biol Rev. 2003 Mar;67(1):86-156.

[2] Cryo-EM structure of the bacteriophage T4 portal protein assembly at near-atomic resolution. Sun L, Zhang X, Gao S, Rao PA, Padilla-Sanchez V, Chen Z, Sun S, Xiang Y, Subramaniam S, Rao VB, Rossmann MG. Nat Commun. 2015 Jul 6;6:7548.

Links:

The Bacteriophage T4 Lab (The Catholic University of America, Washington, D.C.)

Chimera Visualization Software (University of California, San Francisco)

FASEB BioArt (Federation of American Societies for Experimental Biology, Bethesda, MD)

NIH Support: National Institute of Allergy and Infectious Diseases