Abstract
Linking genetic information to population fitness is crucial to understanding living organisms. Despite the abundant knowledge of the genetic contribution to growth, the overall patterns/features connecting genes, their expression, and growth remain unclear. To reveal the quantitative and direct connections, systematic growth assays of single-gene knockout Escherichia coli strains under both rich and poor nutritional conditions were performed; subsequently, the resultant growth rates were associated with the original expression levels of the knockout genes in the parental genome. Comparative analysis of growth and the transcriptome identified not only the nutritionally differentiated fitness cost genes but also a significant correlation between the growth rates of the single-gene knockout strains and the original expression levels of these knockout genes in the parental strain, regardless of the nutritional variation. In addition, the coordinated chromosomal periodicities of the wild-type transcriptome and the growth rates of the strains lacking the corresponding genes were observed. The common six-period periodicity was somehow attributed to the essential genes, although the underlying mechanism remains to be addressed. The correlated chromosomal periodicities associated with the gene expression-growth dataset were highly valuable for bacterial growth prediction and discovering the working principles governing minimal genetic information.
Highlights
Stress-responsive manner[23,24], they were generally regulated in their own specific way in response to environmental changes[25,26]
A novel classification of gene function was performed according to the exponential growth rate of the E. coli strain lacking the corresponding gene
The results showed that the absence of a single nonessential gene triggered either an increase or a decrease in the growth rate, the absence of most genes insignificantly disturbed growth (Fig. 1A)
Summary
Stress-responsive manner[23,24], they were generally regulated in their own specific way in response to environmental changes[25,26]. Our previous study of a genome-reduced strain showed that the expression levels of the genes were either positively or negatively correlated with growth r ates[21]. These results indicated that the expression levels of the individual genes were quantitatively associated with the fitness of the growing bacterial population. Comparative analyses of the growth rates and the transcriptomes were performed to discover the direct linkages among the genes, their expression and cell growth as well as the overall patterns/features of the linkages
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