Technique can ID ‘sick-making’ genes

Scientists have developed a new type of DNA sequence analysis that pinpoints rapidly evolving pathogenic genes and have used the technique to identify hundreds of quickly evolving tubercular and malarial genes believed to represent key points of contact with the human immune system. The work sheds new light on the interaction of lethal organisms with the immune system, and could greatly help researchers in identifying appropriate targets for new drugs or vaccines.

Researchers at Harvard University, Princeton University, the National Institutes of Health, and the University of California, Berkeley, report the findings in the April 29 issue of the journal Nature. Their technique essentially determines the evolutionary stability of genes through the stability of their codons, individual trios of genetic bases such as ACC, GCT, and TTG.

“This technique can be used to quickly identify pathogenic genes that interact closely with the human immune system, since these genes are under tremendous pressure to evolve quickly,” says lead author Joshua B. Plotkin, a junior fellow in the Faculty of Arts and Sciences at Harvard. “Such genes are prime targets for new drugs and vaccines to counter deadly pathogens.”

Plotkin and his co-authors report in the Nature paper on their use of this new method to scan the genomes of parasites responsible for tuberculosis and malaria. The malarial organism, Plasmodium falciparum, has hundreds of genes that are already known to interact closely with the human immune system; a scan of the malarial genome by Plotkin and his colleagues revealed not only these key genes, verifying the technique’s accuracy, but also hundreds of others that had been unknown to scientists. Application of this approach also uncovered numerous key sequences in the genome of the tuberculosis pathogen Mycobacterium tuberculosis.

Plotkin says the new technique could also greatly simplify the identification of critical genes that are conserved, or left intact, by evolution. Researchers are very interested in such genes because they are typically so crucial to an organism that mutant individuals fail to survive. Scanning for conserved genes is currently a labor-intensive process, since researchers need to find homologous genes in many species and then sequence them to assess the degree to which they have been preserved by evolution. By contrast, Plotkin’s new method requires only a single genetic sequence.

The method devised by Plotkin and his colleagues for determining the evolutionary stability of genes is based upon the stability of codons, triplets of genetic bases carved out of the sea of As, Cs, Gs, and Ts that make up the genetic code. Each codon codes for an individual amino acid that makes up proteins. For instance, adjacent thymine, cytosine, and adenine bases – a TCA codon – always yield a serine amino acid.

Plotkin’s team zeroed in on the susceptibility of codons to “point mutations,” which occur when a single DNA base is changed. Point mutations also result in changes to codons, as when TCA switches to TCG. However, not all codon flips have equivalent results: Some codons are more likely to remain coded for the same amino acid as before the mutation, as when CTA changes to CTG, both of which code for leucine; others are prone to switching to a codon that represents a different amino acid, as when AAA is converted to AGA, changing lysine to arginine.

“We found that these so-called ‘volatile codons’ are most likely to occur in genes that are under tremendous evolutionary pressure to change,” Plotkin says. “Conversely, nonvolatile codons tend to be associated with genes that are more stable and are evolving more slowly. It seems almost tautological, but our research showed a clear link between codon and gene stability.”

Plotkin’s co-authors on the Nature paper are Jonathan Dushoff, a postdoctoral researcher at Princeton and the NIH, and Hunter B. Fraser, a graduate student at Berkeley. The work was supported by the Harvard Society of Fellows and the NIH.