Bootstrapping biotechnology: Engineers cooperate to realize precision grammar for programming cells

Researchers at the International Open Facility Advancing Biotechnology (aka, BIOFAB) have just announced that they have, in effect, established rules for the first language for engineering gene expression, the layer between the genome and all the dynamic processes of life. The feat is all the more remarkable considering that just a few years ago several prominent scientists claimed that it would be impossible to develop frameworks enabling reliably reusable standard biological parts.

Collectively, the BIOFAB team has produced thousands of high quality standard biological parts. The DNA sequences that encode all parts and the data about them are free and available online. The project is detailed in three research papers, "Precise and Reliable Gene Expression via Standard Transcription and Translation Initiation Elements," and "Quantitative Estimation of Activity and Quality for Collections of Functional Genetic Elements," published simultaneously in Nature Methods, and "Measurement and Modeling of Intrinsic Transcription Terminators," forthcoming in Nucleic Acids Research.

The BIOFAB's rules for engineering expression come in the form of mathematical models that can be used to predict and characterize the individual parts used in synthetic biology. The work establishes a much-needed technological foundation for the field, allowing researchers to engineer the function of DNA more precisely, and to better predict the resultant behavior.

Dr. Vivek Mutalik, a BIOFAB team leader, says that synthetic biology has been plagued by a lack of reliability and predictability. "Until now, virtually every project has been a one-off -- we haven't figured out how to standardize the genetic parts that are the building blocks of this new field. Researchers produce amazing new parts all the time, but much like trying to use someone else's house key in your own door, it's been difficult to directly reuse parts across projects." Without the ability to characterize parts -- that is, to understand how they will behave in multiple contexts -- biotech researchers are doomed to a lengthy process of trial-and-error. Fortunately, notes Mutalik, "Our work in the BIOFAB changes all that."

The plan for establishing the rules for how genetic parts fit together was ambitious and complex. First, researchers needed to figure out the functional patterns of genetic parts. They had to ask, "To what extent do the basic genetic parts that control gene expression 'misbehave' when reused over and again in novel combinations," said Mutalik. BIOFAB researchers had to make and test hundreds of combinations of frequently used parts, then take the resulting data and build mathematical models that demonstrated part quality.

Joao Guimaraes, a member of the BIOFAB team and graduate student in computational biology, explains that difficult-to-predict parts are deemed to be low quality, while "high quality parts behave the same when reused." Once they found a way to determine part quality, the BIOFAB team set to work on establishing rules for precision control of gene expression, a process that underlies all of biotechnology. They learned by observing natural examples of genetic junctions, and built reliable transcription and translation initiation elements. "We also created standard junctions for transcription terminators, a molecular 'stop sign' for gene expression," said Dr. Guillaume Cambray, a BIOFAB team leader.

While the initial BIOFAB project was able to tame three types of core genetic parts, much more work remains. "We ask that others expand upon the genetic grammar initiated here, to incorporate additional genetic functions and to translate the common rule set beyond E. coli," says Stanford professor and BIOFAB co-director Drew Endy. (Endy also serves as president of the BioBricks Foundation.)

The BIOFAB's seed money came from the National Science Foundation, but this funding came only after 10 years of knocking on doors. Part of the difficulty was that the BIOFAB represented a fundamental engineering research project. It's not the kind of work that is suitable for a single graduate student thesis, and it wasn't economically practical for a biotechnology company to take it on. UC Berkeley professor and BIOFAB co-director Adam Arkin noted that, "We knew that we would only be successful if we could bring together the skills represented by both academia and industry to establish a professional team that could specify and solve the fundamental engineering puzzles that slow the development of effective biotechnologies"

The BIOFAB's collaboration with not only the NSF, but also with industry, has been one of the keys to its success. "Pre-competitive and unrestricted partnerships with industry were essential to guide the work and help secure and extend public funding," said UC Berkeley professor and BIOFAB advisor Jay Keasling. (Both Arkin and Keasling are also affiliated with Lawrence Berkeley Lab; Arkin is Director of the Physical Biosciences Division, and Keasling is an Associate Lab Director for Biosciences.) Other partners came from civil society, including the BioBricks Foundation, a public-benefit organization that helps to advance best practices in the emerging field of synthetic biology. "We were thrilled to help make all BIOFAB engineered parts free-to-use via the BioBrick Public Agreement and the public domain," said Holly Million, the foundation's executive director.

The BIOFAB's standardized parts are specific for E. coli but the "grammar" -- the way in which the rules are constructed for how the parts fit together -- should apply to nearly any organism; many of the BIOFAB's rules for E.coli are expected to apply to other prokaryotes. The initial parts have already begun to have an impact in academic research. Caroline Ajo-Franklin, staff scientist at the Lawrence Berkeley Lab's Biological Nanostructures Facility, noted that her work was able to progress much faster because of the availability of the source code. "We knew we needed a quantitatively characterized library of reliable promoters to move our research efforts forward. Teaming up with BIOFAB changed what would have been at least six months of work into a few weeks."

The BIOFAB's work was supported by the National Science Foundation, the Synthetic Biology Engineering Research Center, Lawrence Berkeley National Laboratory, the BioBricks Foundation, Agilent, Genencor, DSM, and Autodesk.