Spanning high-dimensional expression space using ribosome-binding site combinatorics

Lior Zelcbuch, Niv Antonovsky, Arren Bar-Even, Ayelet Levin-Karp, Uri Barenholz, Michal Dayagi, Wolfram Liebermeister, Avi Flamholz, Elad Noor, Shira Amram, Alexander Brandis, Tasneem Bareia, Ido Yofe, Halim Jubran, Ron Milo

Research output: Contribution to journalArticlepeer-review

128 Scopus citations

Abstract

Protein levels are a dominant factor shaping natural and synthetic biological systems. Although proper functioning of metabolic pathways relies on precise control of enzyme levels, the experimental ability to balance the levels of many genes in parallel is a major outstanding challenge. Here, we introduce a rapid and modular method to span the expression space of several proteins in parallel. By combinatorially pairing genes with a compact set of ribosome-binding sites, we modulate protein abundance by several orders of magnitude. We demonstrate our strategy by using a synthetic operon containing fluorescent proteins to span a 3D color space. Using the same approach, we modulate a recombinant carotenoid biosynthesis pathway in Escherichia coli to reveal a diversity of phenotypes, each characterized by a distinct carotenoid accumulation profile. In a single combinatorial assembly, we achieve a yield of the industrially valuable compound astaxanthin 4-fold higher than previously reported. The methodology presented here provides an efficient tool for exploring a high-dimensional expression space to locate desirable phenotypes.

Original languageEnglish
Pages (from-to)e98
JournalNucleic Acids Research
Volume41
Issue number9
DOIs
StatePublished - 1 May 2013
Externally publishedYes

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