Life history implications of rRNA gene copy number in Escherichia coli

Abstract

The role of the rRNA gene copy number as a central component of bacterial life histories was studied by using strains of Escherichia coli in which one or two of the seven rRNA operons (rrnA and/or rrnB) were deleted. The relative fitness of these strains was determined in competition experiments in both batch and chemostat cultures. In batch cultures, the decrease in relative fitness corresponded to the number of rRNA operons deleted, which could be accounted for completely by increased lag times and decreased growth rates. The magnitude of the deleterious effect varied with the environment in which fitness was measured: the negative consequences of rRNA operon deletions increased under culture conditions permitting more-rapid growth. The rRNA operon deletion strains were not more effective competitors under the regimen of constant, limited resources provided in chemostat cultures. Enhanced fitness in chemostat cultures would have suggested a simple tradeoff in which deletion strains grew faster (due to more efficient resource utilization) under resource limitation. The contributions of growth rate, lag time, Ks, and death rate to the fitness of each strain were verified through mathematical simulation of competition experiments. These data support the hypothesis that multiple rRNA operons are a component of bacterial life history and that they confer a selective advantage permitting microbes to respond quickly and grow rapidly in environments characterized by fluctuations in resource availability.

FIG. 1.

Outline of procedure used to delete the rRNA operon rrnA from the chromosome of E. coli. Homologous recombination events are depicted as crossed dotted lines, which encompass regions of homology; plasmid-derived regions of DNA are depicted in grey.

FIG. 2.

(A) Southern hybridization of PvuII-digested genomic DNA from parental, ΔrrnB, ΔrrnA, and ΔrrnAB strains. Locations of hybridized bands corresponding to the 16S rRNA gene from each rRNA operon (bands A through E, G, and H) are indicated for the parental strain. (B) PCR-amplified rrnA and rrnB regions from each strain. PCR products corresponding to intact rrnA and rrnB operons are approximately 7.4 and 6.7 kb long, whereas deleted rrnA and rrnB operons are much smaller (2.6 and 1.9 kb, respectively). Sizes of markers in lanes M are given (in kilobases) to the right of each panel.

FIG. 3.

Effects of rRNA operon deletions on relative fitness (W) in batch culture. The mean relative fitness of the parental strain (Ara⁺ versus Ara⁻) and of rRNA operon deletion strains (ΔrrnB, ΔrrnA, and ΔrrnAB) versus the parental strain was measured in direct (grey) and simulated (white) batch culture competition experiments. Error bars, standard deviation of the mean (n = 8).

FIG. 4.

Effects of rRNA operon deletions on relative fitness in chemostat culture (dilution rate, 0.11 h⁻¹). The ratios of population densities (rrn deletion strain/parental strain) for ΔrrnA (squares), ΔrrnB (circles), ΔrrnAB (triangles), and parental strains (filled diamonds) (Ara⁺ versus Ara⁻) are plotted as a function of the number of doublings. Error bars, standard errors for four replicate competition cultures.

FIG. 5.

The decreases in relative growth rates (rrn deletion strain/parental strain) for ΔrrnA (squares), ΔrrnB (circles), and ΔrrnAB (triangles) strains are plotted as a function of the growth rate of the parental strain on the same medium (DM+Ac, DM+Glu, LB+Glu). Data points marked with an asterisk represent growth rates significantly different from that of the parental strain (P < 0.05).