A genomics approach to improve the analysis and design of strain selections.

TitleA genomics approach to improve the analysis and design of strain selections.
Publication TypeJournal Article
Year of Publication2008
AuthorsWarnecke, TE, Lynch, MD, Karimpour-Fard, A, Sandoval, N, and Gill, RT
JournalMetabolic Engineering
Volume10
Issue3-4
Start Page154
Pagination154 - 165
Date Published05/2008
Abstract

Strain engineering has been traditionally centered on the use of mutation, selection, and screening to develop improved strains. Although mutational and screening methods are well-characterized, selection remains poorly understood. We hypothesized that we could use a genome-wide method for assessing laboratory selections to design selections with enhanced sensitivity (true positives) and specificity (true negatives) towards a single desired phenotype. To test this hypothesis, we first applied multi-SCale Analysis of Library Enrichments (SCALEs) to identify genes conferring increased fitness in continuous flow selections with increasing levels of 3-hydroxypropionic acid (3-HP). We found that this selection not only enriched for 3-HP tolerance phenotypes but also for wall adherence phenotypes (41% false positives). Using this genome-wide data, we designed a serial-batch selection with a decreasing 3-HP gradient. Further examination by ROC analysis confirmed that the serial-batch approach resulted in significantly increased sensitivity (46%) and specificity (10%) for our desired phenotype (3-HP tolerance).

DOI10.1016/j.ymben.2008.04.004
Short TitleMetabolic Engineering