By Dean A. Haycock

Special to BioWorld Today

One of the doctrines of molecular biology is that only one of the two strands that make up the DNA double helix is transcribed into RNA and translated into a protein. But you can't always depend on doctrines.

This particular one is undermined by the publication of "Protein Encoding by both DNA Strands" in the Feb. 22, 2001, issue of Nature.

Victor Corces and his colleagues at Johns Hopkins University in Baltimore studied the modifier of mdg4 (mod[mdg4]) gene in Drosophila (the fruit fly). This protein must function properly for the fly to develop successfully. It appears to help establish or maintain chromatin, the genetic material of the nucleus.

In most cases, transcription, the reading of genes, proceeds in one direction along one strand of a DNA molecule. This reading produces a molecule of messenger RNA that contains a copy of the genetic information contained in DNA. The messenger RNA is then edited or spliced. Material not useful for making proteins is removed and the remaining transcribed genetic material is joined together.

Lethal Mutations Not So Lethal

The Johns Hopkins scientists had identified two mutations that shut down the mod(mdg4) gene. Each by itself was lethal if inserted into both copies of the gene found in the cells of the fruit fly. Surprisingly, however, if one lethal mutation was inserted into one copy of the gene and a second lethal mutation was inserted into the other copy, the cells still managed to manufacture a usable protein and the flies survived.

The researchers found that fruit fly cells produce two pieces of RNA associated with mod(mdg4). One piece of RNA contains information read from one DNA strand; the other piece of RNA contains information read from the opposite DNA strand. The two pieces of RNA are then joined. The result is a messenger RNA that encodes a single protein. The cell then translates the message contained in the RNA into the crucial protein.

Molecular biologists previously identified genes that can produce more than one protein product. But the process observed in mod(mdg4) transcription, called "trans-splicing," provides another way to produce protein products from a limited number of genes. The authors found that the genetic instructions in one of the DNA strands are read in one direction while the instructions contained in the second DNA strand are read in the opposite direction.

"We ignored all the evidence for maybe three years," Corces said with a laugh. It is easy to understand why. This is the first time trans-splicing has been shown to be responsible for proper functioning of a key protein - although it has been observed in some plant and microbe genomes.

"From the point of view of evolution, this really increases the possibility of the cell making additional proteins from the building blocks it already has," Corces said. "This allows cells to make proteins without any major changes in strategy, as long there is one gene within the intron [a section of DNA that is transcribed into RNA but is not translated into protein] of another gene. And actually this is not a very rare case. There are a lot of genes that are within introns of other genes. Then you can make a hybrid RNA from the two and a hybrid protein. So the question really is: How often does this happen in real life?"

More Than 30,000 Genes In Human Genome?

The surprising finding suggests a new way in which a limited number of genes can generate more proteins. According to Corces, trans-splicing could allow the mod(mdg4) gene to produce more than 20 proteins. Anyone who has been following the progress of efforts to sequence the human genome will immediately see the potential importance of trans-splicing.

"It is interesting with regard to the human genome and the fact that they only find 30,000 genes. Some people are implying that that is not the case," Corces told BioWorld Today. Many biologists were expecting the human genome to contain 80,000 or more genes.

"Some people are thinking that those data are not real, that the reports must be mistaken, that they can only find 30,000 genes because that is what the computer program they use can find," Corces said.

In a statement issued by the press office at Johns Hopkins, Steven Salzberg of The Institute for Genomic Research in Rockville, Md., described the research as "very significant." He added, "It suggests another way we need to look at the genome to look for more proteins. We haven't really been looking for trans-splicing before, and it's another way of generating more proteins from a single gene." He is optimistic that trans-splicing will turn up in the genomes of other organisms.

While Salzberg was not involved in the research described in the Nature paper, he is now developing computational algorithms that could find other examples, according to Corces.

"I don't expect a huge number could come from this [trans-splicing] because the two genes have to be one inside the other going in opposite directions," Corces said. "It is probably happening there but I don't know how many it would add to the 30,000."

The research was funded by the National Institutes of Health in Bethesda, Md. n