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Machines Like Us

Probing the mystery of operon evolution

Sunday, 02 September 2012

The threads of an evolutionary mystery that dates to the birth of molecular biology are beginning to unravel, thanks to a new investigation by computational bioengineers at Rice University and the University of Texas MD Anderson Cancer Center.

In new research published online this week in PLOS Computational Biology, Rice's Oleg Igoshin and MD Anderson's Christian Ray offer a possible explanation for the existence of jointly controlled clusters of genes called operons, which are found in bacterial chromosomes but not in those of higher order organisms like humans.

The new study harkens to one of the earliest 20th-century discoveries in molecular biology, and it could help clear 21st-century hurdles for synthetic biologists.

In the early 1960s, just as scientists were discovering how cells transcribed information from DNA to create the necessary proteins for life, French scientists Jacques Monod and François Jacob found that the bacterium Escherichia coli used three specialized genes to create the proteins it needed to break down and digest lactose. They also found that these three metabolic genes were switched on and off together from a single control point.

Monod and Jacob had discovered the first operon, a set of multiple genes that are controlled as one. It marked the first time that scientists had identified a gene regulatory network, and it earned them a share of the 1965 Nobel Prize in Physiology or Medicine. Monod and Jacob's lac operon turned out to be the first of many bacterial operons. But by the late 1960s, it was clear that operons weren't the biological norm. None have ever been found in humans, for instance, and very few have been identified in multicellular organisms.

"There's never been a definitive explanation for why nature would preferentially select for operons in prokaryotes but not in eukaryotes," said Igoshin, associate professor of bioengineering at Rice. "In addition, we do not know how genes get grouped into operons. Why, for example, are some interacting genes selected to be in one operon while others are not?"

Igoshin and Ray are computational bioengineers who apply mathematics and computational bioinformatics to study cell signaling and other biochemical processes. Ray, a former Rice postdoctoral research associate in Igoshin's research group, is now in the Department of Systems Biology at MD Anderson. Ray and Igoshin began investigating operons in late 2009 to determine whether their evolution might have been influenced by the "noisy" nature of biochemical signals that regulate bacterial gene transcription.

"When a cell is responding to its environment, it can use regulators to control gene expression, but the amount of control that the cell has is limited by the number of molecules like messenger RNAs, which mediate protein production," Ray said. "So, in bacteria, the number of copies of a protein expressed by a gene can vary widely, say from 50 one hour to 100 the next. And this happens even when conditions outside the cell have not changed."