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Fig. 1 | BMC Systems Biology

Fig. 1

From: Reframing gene essentiality in terms of adaptive flexibility

Fig. 1

Project workflow and growth characterizations of false positive strains. a A workflow summarizing the sequence of analyses followed and results from this study. A Keio gene KO collection strain was not available for approximately half of the corresponding false positive genes listed in [13], most likely due to essentiality on rich growth media [22]. Of those strains that were viable in rich media and thus available for a longer growth test, approximately half showed growth in minimal defined media. Those strains that grew were analyzed for mutations. Five false positive strains showed mutations in all replicate experiments sequenced. Four strains showed mixed results, meaning that only some populations accrued mutations. Two strains showed no mutations in any replicate samples. The nine strains that showed mutations in at least some populations were further analyzed in the context of model-predicted alternate pathways and historical data. Six of these cases showed agreement with model-predictions, two showed agreement with previous reports of multi-copy suppression [81], and mutation analysis for one case was not clearly linked to either. b Growth curves of eleven Keio collection strains associated with false positive predictions in defined minimal media. Growth data in terms of cellular density in grams of dry weight per Liter (gDW/L) is reported for the FP gene KO strains. Those strains that accrued mutations in all replicate populations during this growth test are noted with small dashed lines. Those strains that showed mixed results, showing mutations in only some populations, are noted with larger dashed lines. All Keio strains were grown in M9 minimal medium with glucose as the carbon source with the exception of ΔcysK and ΔcysP which utilized a glycerol carbon source. Growth of the wild type strain in glucose and glycerol is also provided as a point of reference (black and grey growth curves)

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