A Taskmaster Transcription Factor

“Researchers showed that a single transcription factor in a tiny, salt-loving archaeon coordinates the expression of more than 100 newly-obtained genes.”

Posted by Elie Dolgin
[Entry posted at 29th June 2009 09:35 PM GMT]

A scattered array of DNA acquired via horizontal transfer can co-evolve into a well-tuned, efficient genetic network to maximize an organism’s fitness, a new study finds. Reporting online earlier this month in Molecular Systems Biology, researchers showed that a single transcription factor in a tiny, salt-loving archaeon coordinates the expression of more than 100 newly-obtained genes.

Halobacterium salinarum
Image: Wikimedia

“It is the first time someone has demonstrated the global integration of recently acquired genes by a single transcription factor,” Nitin Baliga, a microbiologist at the Institute for Systems Biology in Seattle, Wash., who led the study, told The Scientist in an email. “This is an important evolutionary process that impacts all organisms.”

Baliga and his colleagues used a combination of classical genetics, genome-wide approaches, and computational analyses to characterize how the sugar-specific transcriptional regulator TrmB affects metabolism in Halobacterium salinarum, the microbe that gives the Dead Sea its reddish hue. Baliga’s team found that in the absence of glucose or glycerol — two primary carbon sources — TrmB leapt into action and activated or repressed 113 promoters of genes coding for metabolic enzymes.

Of these genes, some were strictly archaeal, but many were shared across all three domains of life. This indicates that some prior gene swapping had taken place and that the gene regulatory network was actively evolving to modulate a proper energy balance. “Acquiring a new function is just the first step,” Baliga said. “Wiring it into an existing complex network so it operates optimally is the next tricky and complex step… What we have discovered is a network undergoing that process.”

Part of that process also involves some pretty complex engineering on the part of the microbe. In a separate study published online in the same journal, Baliga’s team showed that many promoters in Halobacterium evolve inside other coding genes and non-coding RNAs. These overlapping genomic signals “add another layer of complexity” to genomic and transcriptional evolution, Baliga said.

Stephen Busby, a biochemist at the University of Birmingham, UK, who was not involved in the research, called the paper “a great piece of work” but noted that a handful of transcription factors in Escherichia coli also control more than a 100 genes. The study “doesn’t completely surprise me at all,” he said. Baliga conceded that several recent papers have provided “suggestive evidence” for actively evolving transcriptional gene networks, but his group was “the first to put it all together to give a systems perspective.”

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