Boosting Berkeley Lab’s bacteria research

For one summer, Sarah Richardson postponed her work computerizing yeast genome research and probed bacteria instead.

As part of her Department of Energy Computational Science Graduate Fellowship, Richardson served a 2009 practicum under Adam Arkin, director of Lawrence Berkeley National Laboratory’s Physical Biosciences Division. She made important contributions to Arkin’s research into an RNA-based transcription attenuator found in Staphylococcus aureus.

Attenuators are regulatory sequences that halt gene transcription in bacteria and other prokaryotes. The researchers want to make it a standardized tool for fine-grained gene expression control.

“This RNA-regulated attenuator provides an opportunity to, for one, engineer it for better function so it really is an off switch and has a large dynamic range,” Arkin says. Because it blocks transcription, an engineered attenuator might be built into a family of parts operating similarly but orthogonally – without interfering with other functions – in cells, Arkin says.

Attenuators have two pieces, like a lock and key, Richardson says. Arkin’s group wants to modify them so a specific lock works only with a particular key. Two or more could be inserted in the same transcript, working together much like a logic circuit on a computer chip.

Richardson’s practicum focused on improving and augmenting existing computer code to generate new attenuators orthogonal to wild type S. aureus. She learned the Python programming language and wrote an interface between the group’s existing code and the Vienna RNA Package – software designed to predict and compare RNA secondary structures. The bridge made it possible to interchange Vienna with mFold, another RNA secondary structure prediction package, and to compare the two programs’ predictions.

The group’s code starts with the wild-type lock and key and then mutates it. Richardson devised an algorithm to choose a large set of mutually orthogonal or nonorthogonal attenuators from the mutants. She then worked on a cloning technique and lab protocol to synthesize and evaluate proposed attenuators.

Months after Richardson finished her practicum, Arkin’s group was still using software she helped create. The group also improved and automated her lab protocol.