Fig 1.
Inhibitory effect of Kasugamycin on the growth of E. coli MG1655.
Cultures were grown in the presence of different Kasugamycin concentrations, and the optical densities were determined at the indicated times. Three biological replicates were grown, and average values and standard deviations are shown. Empty diamonds: control without Kasugamycin; filled squares: 100 μg/ml; filled triangles: 250 μg/ml; filled circles: 500 μg/ml; asterisks: 750 μg/ml; filled diamonds: 1000 μg/ml.
Fig 2.
Schematic overview of a translatome experiment.
Fig 3.
The distribution of Kasugamycin resistance in the translatome of E. coli.
The KEV value representing a quantitative value of the degree of Kasugamycin resistance was calculated for each of the 2801 analyzed E. coli transcripts as explained in the text. The KEV values were transformed into log2 values, and the number of transcripts was plotted against the resistance.
Table 1.
Transcripts with experimentally-determined 5'-ends and selected features.
Fig 4.
RNA Structure Logos of the groups of Kasugamycin sensitive and Kasugamycin-resistant genes.
For the respective genes 40 nt upstream of the start codon and the first 40 nt of the open reading frames were retrieved from the database EcoGene3. The start codons were removed and the sequences were used to generate RNA Structure Logos at http://www.cbs.dtu.dk/~gorodkin/appl/slogo.html. RNA Structure LOGOS show the deviation of the occurrences of the four nucleotides at any position of a multiple sequence alignment from the statistical expectations based on the respective fractions of the four nucleotieds of the input sequences. The height of the nucleotides corresponds to the degree of deviation. Upright nucleotides have a higher occurrence as expected, inverted nucleotides a lower occurrence. A line indicates the border between the 40 nt upstream and the 37 nt downstream of the start codon. The information content (in bits) of the highest position is indicated A. LOGO of 102 Kasugamycin-sensitive genes (KEVs of < 0.5 in S1 Table). B. LOGO of 137 Kasugamycin-resistant genes (KEVs > 2.0 in S1 Table).
Table 2.
Summary of selected features extracted from RegulonDB, which exhibit differences for the groups of Kasugamycin-sensitive versus—resistant genes.
The number of genes that exhibit the respective feature are listed.