Every choice has its trade-offs. That second slice of pizza might taste good, for example, but it does pack a lot of calories. The low road is easier than the high road, but it’s also longer. Generic brands are cheaper, but they may not be as high quality as name-brand goods. And so on.
While the advantages of many choices are easy to discern, other situations require closer analysis. In a paper just released by mBio, scientists have modeled the economic trade-offs involved in putting genes in an operon, and they’ve shed some light on why it is that microbes like bacteria and archaea so often bundle their genes like this while eukaryotes, for the most part, do not.
Sneppen et al. modeled the economic gains and losses that come from co-transcribing related genes and showed there is a big economic gain to be had in co-transcribing proteins that form complexes together. For these proteins, transcribing one long RNA synchronizes the fluctuations, or noise, in the levels of the different components, reducing component shortfalls. These economic benefits were greater in small organisms like bacteria and archaea than in eukaryotic cells, since smaller cells have fewer mRNA and protein resources.
Sankar Adhya, Head of the Developmental Genetics Section in the Laboratory of Molecular Biology at the National Cancer Institute and a member of mBio’s Board of Editors, also notes that in eukaryotes, each protein usually has a multifunctional role and must be nimble to respond to the multiple signals that stimulate or depress its transcription. Locking up these pleiotropic genes in operons would make transcription less flexible and responsive, he says.
According to Adhya, the study backs up what he has observed in his own work with bacterial transcription. He notes, for instance, that he was much more successful in crystallizing a protein heterodimer when the genes that make the two proteins were moved from their far-flung spots in the bacterial chromosome into a man-made operon. Once the genes were transcribed together, it was much easier to generate the quantities of heterodimer they needed to make a crystal.
The study also emphasizes the economics of evolution, says Adhya, and how these trade-offs are the currency of change. “I think people have ignored this concept that evolution supports economy,” says Adhya.