Innovation and Partnerships Office

Dub-seq: Double Barcoded Shotgun Expression Library Sequencing 2015-160

APPLICATIONS OF TECHNOLOGY:

  • Drug discovery and screening
  • Functional genomics
  • Synthetic biology
  • Enzyme discovery

ADVANTAGES:

  • High throughput
  • Scalable
  • Less labor intensive and expensive than current approaches
  • Enables gene function annotation

ABSTRACT:

Though current functional genomics technologies coupled with next generation sequencing have helped to fill some of the knowledge gap in sequence-to-function space, there is an urgent need for additional high-throughput characterization technologies that are scalable, quantitative, less laborious, cheaper and allow rapid quantification of microbial fitness under hundreds of conditions in different organisms.

A team of researchers at Berkeley Lab (Vivek K. Mutalik, Pavel Novichkov, Adam Deutschbauer, Adam Arkin) has developed a technology for discovering gene functions in microbes. This new method, called Dual Barcoded Shotgun Expression Library Sequencing (Dubseq), combines the shotgun expression library method and next generation sequencing method developed through the ENIGMA program. Dubseq uses dual  random barcoded shotgun expression libraries on replicable plasmids and increases the throughput of functional screens by using barcode sequencing (BarSeq) to assess the microbial fitness.

Researchers have performed proof-of-principle studies in E coli by generating and characterizing Escherichia coli genomic library and profiled this collection using BarSeq under diverse nutrient and stress conditions. This technology will not only support ENIGMA’s mission to connect genes to function, but is also broadly applicable in building a functional compendium of genome fragments from diverse sources.

DEVELOPMENT STAGE: Proven principle.

STATUS: Patent pending. Available for licensing or collaborative research.

SEE THESE OTHER BERKELEY LAB TECHNOLOGIES IN THIS FIELD:

Long-range Barcode Labeled Sequencing for Efficient Genome and Metagenome Assembly