Growth rate regulation in Escherichia coli

Abstract

Growth rate regulation in bacteria has been an important issue in bacterial physiology for the past 50 years. This review, using Escherichia coli as a paradigm, summarizes the mechanisms for the regulation of rRNA synthesis in the context of systems biology, particularly, in the context of genome-wide competition for limited RNA polymerase (RNAP) in the cell under different growth conditions including nutrient starvation. The specific location of the seven rrn operons in the chromosome and the unique properties of the rrn promoters contribute to growth rate regulation. The length of the rrn transcripts, coupled with gene dosage effects, influence the distribution of RNAP on the chromosome in response to growth rate. Regulation of rRNA synthesis depends on multiple factors that affect the structure of the nucleoid and the allocation of RNAP for global gene expression. The magic spot ppGpp, which acts with DksA synergistically, is a key effector in both the growth rate regulation and the stringent response induced by nutrient starvation, mainly because the ppGpp level changes in response to environmental cues. It regulates rRNA synthesis via a cascade of events including both transcription initiation and elongation, and can be explained by an RNAP redistribution (allocation) model.

Fig. 1

Location of seven rrn operons as indicated by capital letters (red) in Escherichia coli chromosome map. The numbers indicate the minute in the map, oriC for the origin of chromosome replication and ter for the terminus of replication. The direction of rrn transcription is indicated by arrows (red) and the bidirectional replication by arrowheads. Only a tiny fraction of E. coli genome encodes for the seven rrn operons.

Fig. 2

(a) The distribution of RNAP is sensitive to environmental cues. During optimal growth, concentrated RNAP (pseudo-colored green) forms dominant transcription foci, which are proposed to be special transcription factories and the nucleolus-like structures, where rRNA is being actively synthesized, in a mid-log cell grown in nutrient rich LB. With the addition of serine hydroxamate (SHX), which caused cell starvation for amino acid and induced the stringent response, RNAP is redistributed relatively homogeneously in the nucleoids. The RNAP is fused with a fluorescent protein and imaged with a fluorescent microscope with the corresponding cells in phase contrast as described (Cabrera & Jin, 2003). (b) Model illustrating the dynamics of the transcription factories or foci and the putative nucleolus-like structures under the two extreme growth conditions. The Escherichia coli chromosome is represented as blue lines folded in loops, the ori of replication as a black square, the seven rRNA operons as large red circles with letters, and two representative tRNA operons as small red circles. The RNAP molecules are represented as small green circles. For simplicity, during optimal growth only two transcription factories/foci and putative nucleolus-like structures, which make the nucleoid more compact by pulling different stable RNA operons into proximity, are indicated (bottom part of the diagram, large green circles encompassing multiple large red cycles labeled 1 and 2) (Adapted from the study by Cabrera & Jin, 2003).

Fig. 3

A typical rrn operon is schematically illustrated. Two promoters (P1 and P2) and terminators (T) for the long rrn transcript are indicated. Blue symbols indicate positive elements for the regulation of rrn, including Fis-binding sites (box) and UP element (UP, star) at the extended P1 promoter region, and antitermination system (AT, triangle) after the P2 promoter. Red symbols indicate negative elements, including H-NS and/or Lrp binding site (box), G/C-rich ‘discrimination sequence’ (GC, circle) at the extended promoter region, and multiple pausing sites (vertical line) before the 16S RNA gene. The illustration is not drawn to scale.

Fig. 4

Model illustrating regulation of rRNA synthesis at system-level in Escherichia coli. RNAP holoenzyme (σR) binds to the rrn P1 promoter (P), forming multiple initiation complexes, including close complex (σRP_c) and open complex (σRP_o). Uniquely, the initiation complexes, particularly open complex, are intrinsically unstable and in rapid equilibrium with each other, before the formation of the stable initially transcribing complex σRP_i in the presence of NTPs. Many positive (blue) and negative (red) elements as indicated control the expression of rrn P1. The activities of RelA and/or SpoT are responsible for the basal level of ppGpp, which are inversely proportional to the nutrient quality of the media and rapid accumulation of high level of ppGpp during starvation. The effects of ppGpp on rRNA synthesis are twofold, including inhibition of initiation, and enhancing pausing of elongation RNAPs, which in turn decreases elongation-induced supercoiling and causes jamming of RNAP at the rrn P1 promoter. Depending on cell growth conditions, released RNAP (R) from rrn operons either rebinds to rrn P1 for reinitiation or redistributes to other non-rrn genome-wide DNA. See text for details.