DNA's protein-building instructions may be able to combine in an unexpected way, increasing the number of possible proteins that can be generated from a given number of genes, according to a report in this week's Nature.
The new finding may have important implications for scientists puzzled by last week's announcement that an initial survey of the human genetic code had found an unexpectedly small number of genes.
Traditional scientific thinking supposes that instructions for building a protein are encoded on one strand of the double-stranded DNA molecule. Researchers at The Johns Hopkins University's Kreiger School of Arts and Sciences identified a fruit fly protein whose instructions follow one strand of the DNA molecule, but also include a segment that follows the opposite strand, which "reads" in the opposite direction.
"We've known for some time that one gene can make multiple protein products," says Victor Corces (pictured at right), chairman of biology and an author of the paper. "The process we're reporting on, which is called trans-splicing, increases even further the possibility of making additional protein products from just two genes."
Trans-splicing had been seen before in a few genes in plant cells and microorganisms, but had never before been shown to be essential to the function of an important protein.
Corces and his co-authors found the trans-splicing while studying the fruit fly gene known as mod (mdg4). They had identified two mutations that could disrupt the function of the gene, and showed that putting either of those mutations in both of the fruit fly's two copies of mod(mdg4) disabled a critical protein made by the gene.
However, when they placed one type of fatal mutation in one copy of the gene and a different kind of fatal mutation in the other copy, the critical protein continued to be made.
"We didn't understand what we were seeing initially, and had assumed it was an error," Corces recalls. But when they took a closer look at how instructions for making the critical protein were put together, they encountered a surprise.
The traditional model of how genes are "read," a process known as transcription, begins when a molecule known as RNA polymerase pries apart DNA, which is shaped like a twisted ladder. RNA polymerase moves in one direction along one strand of the halved ladder, using the stumps of the rungs on that side as a guide for building a molecule called messenger RNA. Messenger RNA later goes through an editing process called splicing that removes various segments and strings the remaining pieces together.
Corces' group found that instructions for building the fruit fly protein appeared to be coming from both strands of DNA. They considered 3 explanations for what they observed. Something might be making RNA polymerase stop and jump from one strand of the DNA to the other. The gene might be rearranging itself to bring all the right sequences to one strand of the DNA. Or both sides of the DNA were being read at once into two different messenger RNA molecules that were later spliced together.
"We found no examples of the first two ideas in the literature, but there were a few references to the third," says Corces. His group later showed that the two mutations occurred on different strands of the DNA molecule. Each copy of the gene could therefore contribute a valid and different part of the protein-making instructions. These parts were then spliced together into the undamaged formula for building the whole protein.
"Interestingly, the instructions on the other DNA strand that are included in this protein may be part of a gene involved in apoptosis, a self-destruct process sometimes triggered in damaged cells," says Corces.
Corces says the finding that the mod(mdg4) can be involved in trans-splicing processes increases the number of proteins that can be made from the gene to more than 20.
"This is a very significant finding, and it suggests another way we need to look at the genome to look for more proteins," says Steven Salzberg, a researcher with joint appointments at Hopkins and The Institute for Genomic Research. "We haven't really been looking for trans-splicing before, and it's another way of generating more proteins from a single gene."
Salzberg, who was not involved in the research presented in this week's Nature, helped write the human genome report published in Science last week. He expressed optimism that trans-splicing will be found in the genetic codes of other organisms.
Other authors on the Nature paper are postdoctoral fellows Mariano Labrador, Fabien Mongelard, and Piedad Plata-Rengifo; Ellen Baxter, a research technician; and Tatiana Gerasimova, a research scientist. Support for this research was provided by the National Institutes of Health.
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