Polymerase Pieces

Researchers discover a new subunit of a bacterial RNA polymerase—as well as hints of its potential role in defending against viruses.

Dec 1, 2014
Jef Akst



The paper
A.N. Keller et al., “ε, a new subunit of RNA polymerase found in Gram-positive bacteria,” J Bacteriol, 196:3622-32, 2014.

The contaminent
Molecular biologist Peter Lewis of the University of Newcastle in New South Wales, Australia, and colleagues were purifying RNA polymerase from the bacterium Bacillus subtilis to study transcription elongation when they stumbled across something they didn’t expect: a small, tagalong protein. “We just simply couldn’t get this protein free from other RNA polymerase subunits no matter what we did,” he says, “which led us to suspect that, at the very least, it’s very tightly associated with RNA polymerase and probably a subunit.”

The investigation
X-ray crystallography of the mystery protein revealed that it was not related to known subunits and therefore deserved its own designation, epsilon (ε). “I think it’s reasonable to call it a subunit,” says microbiologist Richard Gourse of the University of Wisconsin–Madison.

Unknown function
While transcriptomics failed to determine ε’s function—gene expression stayed the same when ε was removed—the protein’s structure was remarkably similar to that of a family of phage proteins involved in inhibiting host cell transcription. Perhaps ε helps protect the bacterium “from phage attack by simply preventing similar phage proteins from binding to RNA polymerase and preventing it from working,” Lewis hypothesizes.

Missing subunits
Although it is unusual to find new RNA polymerase subunits, Andrzej Krezel of Washington University School of Medicine in St. Louis says that this may simply reflect the limited number of model species typically used in science. “In free-living bacteria, and particularly the ones that are less studied so far, I think that additional subunits are quite likely [to] be there.”