MAY 02, 2018 8:17 AM PDT

Chipping Away at the Mystery of Viruses

WRITTEN BY: Carmen Leitch

If an adult gets infected with cytomegalovirus, it usually doesn’t cause any harm, unless that adult is pregnant. In those cases, it's possible for the virus to infect a developing fetus, which can result in birth defects. Now researchers have completed an analysis of the more than 500 viral proteins and peptides that are made after the virus invades a cell. A new bioinformatics tool has revealed this protein profile, which includes 200 proteins that were completely unknown before this. 

Researchers at the Department of Virology of Julius-Maximilians-Universität Würzburg (JMU) in Bavaria, Germany believe that their bioinformatics technique, called PRICE, will have applications in medicine; an understanding of viral proteins may enable scientists to create therapeutics and vaccines for viruses. 

Reporting in Nature Methods, the teams of Professor Lars Dölken and Professor Florian Erhard have created a way to accurately capture the behavior of a cell’s ribosomes, organelles that perform the critical work of assembling proteins. A virus simply hijacks the machinery a cell already contains, so those ribosomes are used to manufacture viral proteins after infection. Molecules called mRNAs take the instructions for assembly from genes to the organelle, where they are translated into proteins. 

There are many questions about the manufacture of viral proteins after a cell is infected. An important technique, ribosomal profiling or Ribo-seq, can help answer those questions. Ribosomal activity, or translation processes, are assessed by Ribo-seq as patterns. PRICE is a better way to identify translation events.

"Previously, a number of error sources often prevented the reliable detection of translation events when analyzing Ribo-seq data," said Erhard. In mRNA, sequences called shorter open reading frames (sORFs) sometimes come before open reading frames (ORFs), which are well known. 

Cytomegalovirus infection of a lung pneumocyte./ Credit: CDC Public Health Image Library

"Our method is capable of resolving even complex cases, for example overlapping ORFs or unusual start codons, with high accuracy. This has allowed us to determine all translated areas genome-wide with high accuracy for the first time," Professor Erhard explained.

The tool allowed the JMU team to find many new cellular and viral proteins and peptides. They also found that many sORF peptides are used on the surface of cells by MHC-1 molecules.

"sORFs thus encode for a new class of antigens that can be recognized by our immune system," said Dölken. "We therefore assume that sORFs are involved in immunological control mechanisms especially during virus infections and stress responses." This work opens new avenues for the investigation of viral infections.

"PRICE now enables us to analyze all existing and future dataset in much greater depth and with substantially improved accuracy," added Dölken. He suggested that it may be worth the effort to take a second look at any data that has already been published. To encourage that effort, the analysis tools have been made freely accessible online by the scientists.

Sources: AAAS/Eurekalert! Via University of Würzburg, Nature Methods

About the Author
  • Experienced research scientist and technical expert with authorships on over 30 peer-reviewed publications, traveler to over 70 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
SEP 20, 2020
Cell & Molecular Biology
Revealing the Structure of Hallucinogens Bound to Their Receptor
SEP 20, 2020
Revealing the Structure of Hallucinogens Bound to Their Receptor
Recent studies have demonstrated that hallucinogenic drugs like LSD, psilocybin, and mescaline have therapeutic potentia ...
OCT 19, 2020
Clinical & Molecular DX
Making Capillary Electrophoresis Accessible for Any Lab
OCT 19, 2020
Making Capillary Electrophoresis Accessible for Any Lab
Analyzing nucleic acids through gel electrophoresis has been a staple of genetic research for decades. But using traditi ...
OCT 19, 2020
Cell & Molecular Biology
Mapping the Human Proteome
OCT 19, 2020
Mapping the Human Proteome
To learn more about biology and medicine, researchers have used advances in molecular techniques and computational biolo ...
OCT 07, 2020
Neuroscience
Biocompatible Gel Restores Sciatic Nerve Function in Rats
OCT 07, 2020
Biocompatible Gel Restores Sciatic Nerve Function in Rats
Video: Explains poly(lactic-co-glycolic acid), a hydrogel biopolymer that is a similar concept to the new hydrogel built ...
NOV 19, 2020
Cell & Molecular Biology
A Different View of Chromosomes
NOV 19, 2020
A Different View of Chromosomes
Many of us are familiar with typical diagrams of a chromosome, which is usually drawn like a stubby X. While that pictur ...
DEC 01, 2020
Cell & Molecular Biology
Protein Biology Takes a Giant Leap Into the Future
DEC 01, 2020
Protein Biology Takes a Giant Leap Into the Future
The genome has instructions for creating and maintaining an organism, but most biological functions involve their transl ...
Loading Comments...