Figure 1.
Regression of tRNA Isoacceptor Concentrations at the Highest Measured Growth Rate for E. coli Strain W1485 (A K12 Derivative) against the Same at Lower Growth Rates
tRNA concentrations at the highest growth rate (μ = 2.5 doublings/h) are regressed against the same at (A) μ = 0.4 doublings/h and at (B) μ = 0.7 doublings/h. Concentration data are from [2]. Classification into “major,” “minor,” and “neither” types is from codon usage in ribosomal protein genes and anticodon reading relationships from [2,9]. All isoacceptors increase with growth rate, so that the uniform increase of all isoacceptors swamps variation in increase of individual isoacceptors.
Figure 2.
Frequency Histograms and Density Estimates for the Ratio Increase in Concentration of Different Classes of Isoacceptors After an Increase in Growth Rate
Isoacceptors are grouped into “major,” “minor,” and “neither” classes, and the distributions of concentration ratios are shown for each class after an increase in cellular growth rate (A, light grey) from 0.4 to 2.5 doublings/h and (B, dark grey) from 0.7 to 2.5 doublings/h. White-colored bars correspond to values for Thr1+Thr3 as labeled (see text). While no difference is evident among classes from 0.4 to 2.5 doublings/h, a slight difference is evident from 0.7 to 2.5 doublings/h. This difference is not significant but becomes significant if Thr1+Thr3 and Pro1+Pro3 are removed from analysis, or trimmed means are used to compare groups.
Table 1.
tDNA Operons in the E. coli K12 Genome
Figure 3.
Effect of Clustering Radius on the Number of tDNA Clusters Obtained in the E. coli K12 Genome (Calculated in Steps of 25 bp)
Clustering radius (r) is the maximum distance from one end of a tDNA in bp within which part of another co-linear tDNA must fall to be joined into the same cluster. Vertical dashed line shows the value used in this study (r = 300 bp), which correctly recovered all but three of the 44 experimentally known tDNA operons (indicated by horizontal dashed line). These three, ribosomal operons all, were not correctly recovered until a much higher radius was used but then within only a narrow range (2,400 ≤ r ≤ 2,800 bp) before a false positive was encountered. Thus, the natural proximity of tDNAs within operons made it possible through tDNA coordinates and strandedness alone to recover most of the true operons in E. coli K12.
Table 2.
Constraints Added for Least Squares Estimation of OSCs
Table 3.
Comparison of Gene and Operon Models for Explaining tRNA Concentrations in E. coli, and Circular Regressions of the Estimated OSCs on Angle (α), Increasing as in min, but with the Origin of Replication at Zero in the E. coli K12 Genome
Figure 4.
Residuals of the Operon Model Regressions Used to Estimate Expression (Without Intercept), Showing Unexplained Variation
Only residuals with absolute values larger than 10−14 are shown. Thus, variation in all but nine of the 44 operons is completely explained. All operons containing tDNAs with these non-zero residuals are arrayed at the bottom, showing true tDNA order from 5′ to 3′. All such tDNAs are in single-copy except for the genes encoding Ala1B in the ribosomal operons, indicated by vertical stacking at the bottom, Arg3, which is repeated three times in the serV operon, and MetM, Gln1, and Gln2, which are each repeated twice in the metT operon (for its true configuration, see Table 1). Residuals are shown in μM units, those of standardized concentrations. Residuals are shown for each tDNA in order of increasing growth rate from 0.4 (leftmost) to 2.5 doublings/h (rightmost). Positive (negative) residuals indicate underestimation (overestimation) by the model.
Table 4.
Evidence for Log-Linear Fit of Estimated OSCs (μM) against Genome Location (m)
Figure 5.
Total Expression (Bulk Output) at μ = 2.5 Doublings/h of tDNA Operons Against Their Location in the E. coli K12 Genome
The angular scale is symbolized by α in the text, with 0° placed at the origin of replication (oriC) shown at the top. Units of the radial axis (expression) are initiations per min per picogram of culture mass. Leading strand operons are indicated in blue and lagging strand operons in gold. The red curve shows a re-estimated circular regression of all the data including only intercept and cosine terms, showing the significant tendency of expression to increase toward oriC, especially for leading strand operons. Values for lagging strand operons asnV, asnU, and asnT are covered but equal by constraint (see Table 2) to the value for asnW.
Table 5.
Estimated Average Synthesis Rates Per Operon (Number of Transcripts Initiated per min per Copy) of tRNA Precursors in the E. coli K12 Genomea
Figure 6.
Ratio Increase in Per-Copy Synthesis Rates of Operons (Promoter Velocities) as Growth Rate Increases from μ = 0.4 to 2.5 Doublings/h
(A) μ = 0.7 to 2.5 doublings/h. (B) Against fractional distance from the origin of replication oriC with maximum distance set at 1 (m). Outlying values for ileX and ileY are indicated.