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Agile BioFoundry


EMSL Project ID
50421

Abstract

This proposed EMSL Resource Owner project, is a sub-project supporting two DOE-EERE-BETO supported PNNL projects: FY16-17 four-national laboratory “Agile BioFoundry” (ABF) seed project and a larger FY17-19 nine-national laboratory ABF project. PNNL’s effort for these projects, which includes the analytical work proposed in this Resource Owner’s project as well as strain development at the BSEL will support Task 1 of both ABF multi-lab projects. The objective of the multi-lab projects is to establish a distributed Synthetic Biology Foundry (known as the Agile BioFoundry (ABF), through a consortium of nine national laboratories, that will productionize synthetic biology by integrating advanced biological engineering with computing, overall process analysis, and scale-up. This effort will establish a differentiated and unique capability that will enable BETO to meet its goals for more cost-effective production of bio-based fuels and products through a 40% increase in efficiency of biological process development and a 50% reduction in time-to-market.

This EMSL project will provide analytical results from leading edge analytical biology, both GC and LC mass spectrometry and 13C metabolic flux analysis (13C MFA). These analytical results are required for monitoring proteins and metabolites for assessing the impact of introducing new pathways into host organisms through identification of host genomic modifications necessary to relieve bottlenecks in the production of adipic acid and other target products of the projects. The analytical results from this EMSL project will provide guidance for the PNNL strain development effort conducted at the BSEL and to the strain development efforts at the partner national laboratories for the two ABF projects. Successful application of the EMSL-generated results will demonstrate the important role that these EMSL analytical capabilities can play in enabling the rapid engineering cycles necessary for competitive development of new production hosts and pathways. This EMSL project will showcase EMSL analytical biology capabilities and demonstrate their usefulness to the broader research community. The PNNL portion of the large multi-lab ABF project also provides an opportunity to demonstrate the benefits merging EMSL and BSEL capabilities for the success of a collaborative research project can afford. It is expected that the results of the ABF project will be of interest to, and will have application for, entities interested in development of production hosts such as enzyme companies, biofuel companies, biochemical companies, academics, and national laboratory scientists. Distribution of the results of this project will be through communications conducted through a variety of channels including technical publications and presentations at conferences, along with direct pursuit of opportunities to explore the potential for collaborations with industrial partners who potentially could apply the findings of this project to their own process development efforts. Engaging industry for technology transfer is written into the operating plan for the ABF project.

Project Details

Start Date
2018-07-24
End Date
2020-09-30
Status
Closed

Team

Principal Investigator

Scott Baker
Institution
Environmental Molecular Sciences Laboratory

Team Members

Marco Forgia
Institution
University of Turin

Nathalie Munoz Munoz
Institution
Environmental Molecular Sciences Laboratory

Jeremy Zucker
Institution
Pacific Northwest National Laboratory

Mark Butcher
Institution
Pacific Northwest National Laboratory

Thomas Fillmore
Institution
Environmental Molecular Sciences Laboratory

Young-Mo Kim
Institution
Pacific Northwest National Laboratory

Carrie Nicora
Institution
Pacific Northwest National Laboratory

Kristin Burnum-Johnson
Institution
Environmental Molecular Sciences Laboratory

Jon Magnuson
Institution
Pacific Northwest National Laboratory

Errol Robinson
Institution
Pacific Northwest National Laboratory

Weijun Qian
Institution
Pacific Northwest National Laboratory

Thomas Metz
Institution
Pacific Northwest National Laboratory

Ellen Panisko
Institution
Pacific Northwest National Laboratory

Marat Valiev
Institution
Environmental Molecular Sciences Laboratory

Related Publications

Geiselman G.M., X. Zhuang, J. Kirby, M. Tran-Gyamfi, J. Prahl, E.R. Sundstrom, and Y. Gao, et al. 2020. "Production of ent-kaurene from lignocellulosic hydrolysate in Rhodosporidium toruloides." Microbial Cell Factories 19. PNNL-SA-150034. doi:10.1186/s12934-020-1293-8
Li X., Y. He, L. Zhang, Z. Xu, H. Ben, M.J. Gaffrey, and Y. Yang, et al. 2019. "Discovery of Potential Pathways for Biological Conversion of Poplar Wood to Lipids by Co-Fermentation of Rhodococci Strains." Biotechnology for Biofuels 12. PNNL-SA-136201. doi:10.1186/s13068-019-1395-x