For decades, no one knew how a virus that preys on bacteria transfers its DNA into the host cells because it appeared to lack the structures other viruses use for that process. Now researchers have discovered how the virus does it – using a structure that might hold applications for nanotechnology.
Researchers have discovered a tube-shaped structure that forms temporarily in a certain type of virus to deliver its DNA during the infection process and then dissolves after its job is completed. The tube is long enough to span the inner and outer cell membranes of an E. coli bacterium, bridging the “periplasmic space” in between. (Image: Lei Sun/Purdue University)
A stereo image of the protein helices that assemble to form the DNA-transmitting tube.
The inside of the protein tube is lined with a particular amino acid (glutamine) that has DNA-binding properties along its entire length, the researchers discovered. Their orientation strongly suggests that DNA transport is unidirectional, according to Bentley Fane of the UA’s BIO5 Institute. “The glutamine side chains remind me of the teeth found in the mouth of a giant sea lamprey, which also appears to be a one-way passage,” Fane said (see next image). (Image courtesy of Bentley Fane)
The inside of the virus’ protein tube appears to be equipped with molecules that grasp DNA and funnel it along the one-way passage, analogous to the teeth found in the mouth of a giant sea lamprey as pictured here.
A research team led by the University of Arizona and Purdue University has discovered something very unique about a virus that has been studied for decades: It has the ability to grow a temporary tube-shaped structure, enabling it to inject its DNA into the bacteria on which it preys.
The finding solves an almost century-long mystery.
Typically, a virus will use a tail-like structure to deliver its DNA. The question was how that transfer happened in viruses with no apparent “tail.” The explanation was found by examining phiX174, a bacteriophage that preys on E. coli bacteria, which is able to grow a tube-like structure to do the job – and then disassemble that structure after infection.
The discovery, published in the journal Nature, represents the first known viral DNA-transmitting structure that has been decoded at the atomic scale and could hold implications for nanotechnology and medical research.
Most bacteriophages, as viruses that specifically attack bacteria are called, have a tail-like structure that they use to attach to the bacteria’s cell wall, punch a hole in it and insert their own genetic material in an effort to hijack the cell’s machinery to produce more viruses. Not so phiX174, a bacteriophage that preys on E. coli bacteria. This bacteriophage is in a class of viruses that do not contain an obvious tail section for the transfer of its DNA into host cells
“Since this virus was discovered in the 1920’s, no one knew how the DNA got into the cell,” saidBentley Fane, a professor in the Department of Plant Sciences in the UA College of Agriculture and Life Sciences, “because phiX doesn’t have a visible tail.”
“But, lo and behold, it appears to make its own tail,” said Michael Rossmann, the Hanley Distinguished Professor of Biological Sciences at Purdue University, who led the research project together with Fane. “It doesn’t carry its tail around with it, but when it is about to infect the host it makes a tail.”
Researchers were surprised to discover the fleeting tail.
“This structure was completely unexpected,” said Fane, who also is a member of the BIO5 Institute. “No one had seen it before because it quickly emerges and then disappears afterward, so it’s very ephemeral.”
It turns out the components for the tail structure are packaged inside the virus’ protein shell and the tail is assembled on the surface of the bacterial cell, Fane explained.
“There was no known example of a virus that builds a tube on the surface of the host cell,” he said.
Fane’s research group at the BIO5 Institute mutated the virus so that it could not form the tube.
“We made mutations in the gene coding for the protein that make up the tube that would prevent them from coming together to form a tube,” Fane said. “Our hypothesis was that the virus particle would assemble in the cell, but that particle would be noninfectious because it couldn’t form a tube.”
The results, he said, came out like a textbook test of a hypothesis.
“The mutated viruses were indistinguishable from their normal counterparts, but they were unable to infect host cells because they couldn’t get their DNA inside.”
In addition, the researchers made direct observations of the fleeting tubes using an extremely powerful electron microscope in Rossmann’s lab at Purdue, in a technique called cryo electron tomography.
“It took us a few months to work out all the parameters,” Fane said, “because the tubes are so small, right at the limit of what you can see with this technique.”
The team managed to obtain images showing the viruses attached to the bacteria and the tube penetrating all the way through the bacterial cell wall. E. coli cells have a double membrane, and the researchers discovered that the two ends of the virus’s protein tube attach to the host cell’s inner and outer membrane.
Images created using cryo electron tomography show this attachment. The protein tube was shown to consist of 10 “alpha-helical” molecules coiled around each other. Findings also showed that the inside of the tube contains a lining of amino acids that could be ideal for the transfer of DNA into the host.
“This may be a general property found in viral-DNA conduits and could be critical for efficient genome translocation into the host,” Rossmann said.
According to Fane, the discovery has potential implications for nanotechnology.
“What we have here is a nanotube made by nature,” Fane said, “a protein structure that evolved to carry out a very specific function. I could think of lots of applications that translational scientists could develop from this. The tube seems to be ideally suited for transporting DNA, and its structure suggests you could easily make it longer or shorter. Perhaps one could use it as a template to crystallize metal onto it, or use it to transport molecules between cells.”
Although this behavior had not been seen before, another phage called T7 has a short tail that becomes longer when it is time to infect the host, said Purdue postdoctoral research associate Lei Sun, the lead author of the research paper.
The paper’s other authors are UA research technician Lindsey N. Young; Purdue postdoctoral research associate Xinzheng Zhang; former Purdue research associate Sergei P. Boudko; Purdue assistant research scientist Andrei Fokine; Purdue graduate student Erica Zbornik; Aaron P. Roznowski, a UA graduate student; and Ian Molineux, a professor of molecular genetics and microbiology at the University of Texas at Austin.
The research has been funded by the National Science Foundation, U.S. Department of Energy, and the U.S. Department of Agriculture.