Berkeley Lab

ENIGMA Team Anchors Collaboration to Accelerate Experiment-based Gene Function Assignments

As part of a large scale collaboration, a diverse team of scientists from ENIGMA — a Scientific Focus Area at Lawrence Berkeley National Laboratory (Berkeley Lab) — and other institutions lead by Adam Arkin (APA) as Technical Co-Manager, as well as researchers at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), have developed a workflow that enables large-scale, genome-wide assays of gene importance across many conditions. Released in the journal Nature, “Mutant Phenotypes for Thousands of Bacterial Genes of Unknown Function,”  describes the identification of mutant phenotypes for thousands of bacterial genes that have no currently known function. Read more at LBL News Center.

From back row left: Adam Deutschbauer, Jen Kuehl, Hualan Liu, Romy Chakraborty, Astrid Terry, Jayashree Ray, Morgan Price, and Hans Carlson. Missing from the picture: Adam Arkin, Kelly Wetmore, Judy Wall, Grant Zane et al

The ENIGMA team was brought together from multiple institutions/labs through the vision of Adam Arkin to work together on mission critical science under the leadership of Adam Deutschbauer and Morgan Price (Arkin Lab) including the support of Kelly Wetmore (Arkin Lab Graduate Student), Jennifer Kuehl (Arkin Lab), Hualan Liu (Deutschbauer Lab),  Romy Chakraborty, Jayashree Ray(Deutschbauer Lab), Hans Carlson (Deutschbauer Lab), Judy Wall, Grant Zane (Wall Lab), JGI’s Matthew Blow and other collaborators.

Deutschbauer lab is  expert in microbiology, genetic technology development, high throughput culturing and quantitative assessment of microbial growth under diverse conditions; the Blow lab (co-corresponding) and JGI are expert in application of advanced sequencing technologies to assessment of biological function; the Arkin lab is expert in microbial biotechnology, systems and synthetic biology, and biological data science. The Chakraborty lab is expert in environmental microbiology and isolation and characterization of microbes. The Wall lab is expert in microbial genetics, biochemistry and physiology.

With the analysis/interpretation support tools http://fit.genomics.lbl.gov/ developed by Morgan Price integrated into ENIGMA’s resource pipeline, the next steps will be to transfer these technologies to fungi with collaborating UC Berkeley scientist Jeff Skerker (Arkin Lab), apply new genetic technologies such as DUB-SEQ developed by ENIGMA research scientist Vivek Mutalik (R&D 100 winner! Arkin Lab), and the Arkin Lab’s growing expertise with CRISPR techniques, to significantly accelerate functional analysis of microbes. — There are opportunities here both to innovate in the technology and apply it to well-chosen diversity in more informative and DOE relevant environments.

ENIGMA team bolded: Morgan N. Price1, Kelly M. Wetmore1, R. Jordan Waters2, Mark Callaghan1, Jayashree Ray1, Hualan Liu1, Jennifer V. Kuehl1, Ryan A. Melnyk1, Jacob S. Lamson1, Yumi Suh1, Hans K. Carlson1, Zuelma Esquivel1, Harini Sadeeshkumar1, Romy Chakraborty3, Grant M. Zane4, Benjamin E. Rubin5, Judy D. Wall4, Axel Visel2,6, James Bristow2, Matthew J. Blow2,*, Adam P. Arkin1,7,*, Adam M. Deutschbauer1,8,*

1Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory
2Joint Genome Institute, Lawrence Berkeley National Laboratory
3Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory
4Department of Biochemistry, University of Missouri
5Division of Biological Sciences, University of California, San Diego
6School of Natural Sciences, University of California, Merced
7Department of Bioengineering, University of California, Berkeley
8Department of Plant and Microbial Biology, University of California, Berkeley

Funding for the development of the microbiology and initial technology was supported by the ENIGMA “Discovery Program”; where high risk projects are funded for a short duration to encourage high impact changes in science or technological capability that extend and enhance our ongoing research; and the sequence for the study was enabled by the JGI Community Sequencing project for the broad application to microbes of DOE Community interest.