Researchers analyzed patterns of codon usage across 74 bacteriophages using the concept of a "genome landscape," a method of visualizing long-range patterns in a genome sequence.
Their findings extend the translational theory of codon bias to the viral kingdom, demonstrating that the viral genome is selected to obey the preferences of its host.
“The host bacterium is exerting a strong evolutionary pressure on the virus,” Joshua Plotkin, lead author and assistant professor in the Department of Biology at Penn, said. “This happens because a virus must hijack the machinery of its host in order to reproduce. We are seeing that viruses are forced to adopt the particular codon choices preferred by the bacterium they infect.”
The study found that each bacterium has a preferred way of spelling its genes. And it appears that viruses that infect a bacterium spell their own genes in the same way the bacterium does, obeying the rules of its host and demonstrating co-evolutionary behavior.
“Like a bee and a flower, an example of co-evolution between two large organisms, the same fundamental biological processes operate between two small organisms, as reflected in their genome sequences,” Plotkin said.
Moreover, the team found that the degree of codon bias varies across the viral genome. By comparing the observed genomes to randomly drawn genomes, the team demonstrated that the regions of high codon bias in these viral genomes often coincide with regions encoding structural proteins. Thus, the proteins that a virus needs to produce at high levels utilize the same encoding as its host organism does for highly expressed proteins.
Any protein can be encoded by multiple, synonymous spellings, but organisms typically prefer one spelling over others, a phenomenon known as codon bias. Codon bias is generally understood to result from selection for the synonymous spelling that maximizes the rate and accuracy of protein production.
The study, appearing in the current issue of the journal Public Library of Science Computational Biology, was performed by Plotkin and Grzegorz Kudla of the Department of Biology in the School of Afrts and Sciences at Penn and Julius Lucks and David Nelson of Harvard University.
The study was supported by grants from the Burroughs Wellcome Fund and the National Science Foundation.
Jordan Reese | EurekAlert!
Novel mechanisms of action discovered for the skin cancer medication Imiquimod
21.10.2016 | Technische Universität München
Second research flight into zero gravity
21.10.2016 | Universität Zürich
Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.
"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...
In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.
A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...
By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.
"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...
COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.
In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...
'Ferroelectric' materials can switch between different states of electrical polarization in response to an external electric field. This flexibility means they show promise for many applications, for example in electronic devices and computer memory. Current ferroelectric materials are highly valued for their thermal and chemical stability and rapid electro-mechanical responses, but creating a material that is scalable down to the tiny sizes needed for technologies like silicon-based semiconductors (Si-based CMOS) has proven challenging.
Now, Hiroshi Funakubo and co-workers at the Tokyo Institute of Technology, in collaboration with researchers across Japan, have conducted experiments to...
14.10.2016 | Event News
14.10.2016 | Event News
12.10.2016 | Event News
21.10.2016 | Health and Medicine
21.10.2016 | Information Technology
21.10.2016 | Materials Sciences