Washington, April 22 : Ohio State University scientists have come up with an experimental approach that may facilitate the identification of specific structural parts of a viroid, pathogens that can kill or damage food crops and other plants.
Biao Ding, professor of plant cellular and molecular biology at the university, says that susceptible plants can be prevented from viroid infections by genetically altering them, given that no chemical treatments exist that can specifically inhibit viroid multiplication and spread.
And the best approach to such bioengineering can be realised by learning exactly how the pathogens function in the first place, he adds.
"We're trying to understand how the infection occurs, and how the RNA propagates itself in the cell. But more importantly, even for human diseases, is discovering how a disease spreads. That's where the problem comes in the plant," Ding said.
According to background information in a report in the journal The Plant Cell, viroids resemble viruses, but consist of only small RNA molecules that do not have the protein coat found on viruses, and that do not encode any proteins.
The report also reveals that so far, viroids have been shown to infect only plants. It says that about 30 species of viroids exist that affect such plants as tomatoes, potatoes, palm trees and chrysanthemums.
"The scientist who discovered the first viroid spent many years trying to find the pathogen. It's not bacteria. It's not a virus. It is really its own kind of pathogen. It doesn't make any proteins or have any protein coat. It's just a piece of RNA," Dr. Ding said.
He and his colleagues introduced mutations to specific points within the viroid RNA to see how such disruption affected the role of each piece of the structure.
Although the researchers did not get any answer to explain the entire viroid RNA function, their approach showed promise for expanding knowledge about how RNA works in the development of an organism and in the spread of multiple diseases, Ding said.
The researchers say that unlike the DNA structure, a double helix with base pairs of nucleotides connecting the strands, many RNAs are formed by a single strand that folds back in on itself. As a result, the RNA structure has a series of loops that scientists have long assumed were empty holes with unclear roles in the RNA function, they add.
The team says that recent experiments have shown that many of such loops are not holes, but are actually the most important structural parts of the RNA.
"Those loops interact with proteins, other RNAs and small molecules. That helped us decide to look at all of the loops of a viroid RNA and see how each one functions," Ding said.
The viroid model used for this research is called the Potato spindle tuber viroid, and its infection was studied in a tobacco-like plant called Nicotiana benthamiana for the experiment.
Lead study author Xuehua Zhong, who was a graduate student when the study was conducted, led the work to introduce mutations to each of the 27 loops in this viroid to disrupt its structure. The objective behind the work was to see how that disruption affected either viroid replication or the viroid's ability to spread, or both actions in the case of some loops.
"It looks like all 27 loops are important, but we need to know which ones are important for the RNA's ability to reproduce itself in the cell, and which ones are important for spreading from one part of the plant to another. And we know we can find similar structures in different RNAs, so that means that what we learned can be applied to other types of RNA," Zhong said.
So far, the researchers have found that except for one loop, a change to almost any loop slows or eliminates replication. They have also identified a few loops that are required for movement of the viroid from one part of the plant to another, which spreads the infection.
"We still don't know exactly where a particular mutant fails to spread because there are so many cell layers in the plant. We still need to take a look at each mutant to see where the infection starts in the plant and what kind of cell types are affected," Ding said.
He further said that the viroids themselves do not contain or make proteins, and that there must be proteins in the plant that are responsible for recognizing the viroid and allowing it to move around.
The researcher said that the viroid mutants that fail to replicate or move around would be valuable materials to help identify these proteins.
"Once you pinpoint a protein, you might be able to change the protein function so it cannot recognize the viroid and allow it to spread," said Ding, whose lab is developing methods to look for all of the proteins that bind to viroids to promote infection.
"This is really just the beginning. This is a new focus, not just for us, but for other researchers studying RNAs that can be analyzed in similar ways because their structure is the same or similar. This is really a new way of investigating," Ding said.