PMID:20639866
| Citation |
Warner, JR, Reeder, PJ, Karimpour-Fard, A, Woodruff, LB and Gill, RT (2010) Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat. Biotechnol. 28:856-62 |
|---|---|
| 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 (beta-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. |
| Links |
PubMed Online version:10.1038/nbt.1653 |
| Keywords |
Base Sequence; Computational Biology/methods; DNA Barcoding, Taxonomic; Escherichia coli/genetics; Escherichia coli/growth & development; Escherichia coli/metabolism; Escherichia coli Proteins/genetics; Escherichia coli Proteins/metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Gene Library; Genetic Engineering/methods; Genome, Bacterial/genetics; Molecular Sequence Data; Mutation; Oligonucleotide Array Sequence Analysis; Oligonucleotides/chemical synthesis; Oligonucleotides/chemistry; Oligonucleotides/genetics; Recombination, Genetic; Sequence Analysis, DNA |
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