A genomics approach to improve the analysis and design of strain selections |
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Authors: | Warnecke T E Lynch M D Karimpour-Fard A Sandoval N Gill R T |
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Affiliation: | aDepartment of Chemical and Biological Engineering, University of Colorado, ucB424/ECCH120, Boulder, CO, USA;bOpX Biotechnologies, Boulder, CO, USA |
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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). |
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Keywords: | 3-Hydroxypropionic acid Tolerance Selection Strain engineering Multi-SCale Analysis of Library Enrichments (SCALEs) |
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