Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides

Abstract

A fundamental goal in biotechnology and biology is the development of approaches to better understand the genetic basis of traits. Here we report a versatile method, trackable multiplex recombineering (TRMR), whereby thousands of specific genetic modifications are created and evaluated simultaneously. To demonstrate TRMR, in a single day we modified the expression of >95% of the genes in Escherichia coli by inserting synthetic DNA cassettes and molecular barcodes upstream of each gene. Barcode sequences and microarrays were then used to quantify population dynamics. Within a week we mapped thousands of genes that affect E. coli growth in various media (rich, minimal and cellulosic hydrolysate) and in the presence of several growth inhibitors (β-glucoside, D-fucose, valine and methylglyoxal). This approach can be applied to a broad range of traits to identify targets for future genome-engineering endeavors.

DOI: 10.1038/nbt.1653

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@article{Warner2010RapidPO, title={Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides}, author={Joseph R Warner and Philippa J. Reeder and Anis Karimpour-Fard and Lauren B.A. Woodruff and Ryan T. Gill}, journal={Nature Biotechnology}, year={2010}, volume={28}, pages={856-862} }