Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast

Drew G. Michael, Ezekiel J. Maier, Holly Brown, Stacey R. Gish, Christopher Fiore, Randall H. Brown, Michael R. Brent

Research output: Contribution to journalArticlepeer-review

25 Scopus citations


The ability to rationally manipulate the transcriptional states of cells would be of great use in medicine and bioengineering. We have developed an algorithm, NetSurgeon, which uses genomewide gene-regulatory networks to identify interventions that force a cell toward a desired expression state. We first validated NetSurgeon extensively on existing datasets. Next, we used Net-Surgeon to select transcription factor deletions aimed at improving ethanol production in Saccharomyces cerevisiae cultures that are catabolizing xylose. We reasoned that interventions that move the transcriptional state of cells using xylose toward that of cells producing large amounts of ethanol from glucose might improve xylose fermentation. Some of the interventions selected by NetSurgeon successfully promoted a fermentative transcriptional state in the absence of glucose, resulting in strainswith a 2.7-fold increase in xylose import rates, a 4-fold improvement in xylose integration into central carbon metabolism, or a 1.3-fold increase in ethanol production rate. We conclude by presenting an integrated model of transcriptional regulation and metabolic flux that will enable future efforts aimed at improving xylose fermentation to prioritize functional regulators of central carbon metabolism.

Original languageEnglish
Pages (from-to)E7428-E7437
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number47
StatePublished - Nov 22 2016


  • Engineering
  • Gene-regulatory networks
  • Regulatory systems biology
  • Saccharomyces cerevisiae
  • Transcriptome


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