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Bacterial Adaptation through Loss of Function

Figure 4

Identification and characterization of transposon insertion locations that alter fitness in single amino acid media.

(A) A library of ∼500,000 independent transposon insertion mutants [21] was grown for ∼20 generations in defined media with a single amino acid carbon source. Serial dilutions were used to keep the cultures in exponential phase. To characterize the distribution of transposon insertion locations in the population, DNA adjacent to the transposons was amplified, labeled, and hybridized to a custom ORF microarray. (B) K-means clustering was used to organize the fitness profiles of 809 genes in whose vicinity transposon insertions significantly altered fitness in at least one media (see Materials and Methods). Each row represents a gene; each column contains data from a different biological replicate. Values compare the fraction of mutants with transposon insertions in or near each gene before (finitial) and after (ffinal) growth in single amino acid media. Yellow (blue) indicates an increase (decrease). (C) Shown are functional enrichments and depletions based on Gene Ontology annotations that iPAGE [24] identified in the clusters from (B) and the genes not in any cluster (‘Other’). ECA: enterobacterial common antigen.

Figure 4