Increased RNA polymerase availability directs resources towards growth at the expense of maintenance

Abstract

Nutritionally induced changes in RNA polymerase availability have been hypothesized to be an evolutionary primeval mechanism for regulation of gene expression and several contrasting models have been proposed to explain how such 'passive' regulation might occur. We demonstrate here that ectopically elevating Escherichia coli RNA polymerase (Esigma(70)) levels causes an increased expression and promoter occupancy of ribosomal genes at the expense of stress-defense genes and amino acid biosynthetic operons. Phenotypically, cells overproducing Esigma(70) favours growth and reproduction at the expense of motility and damage protection; a response reminiscent of cells with no or diminished levels of the alarmone guanosine tetraphosphate (ppGpp). Consistently, we show that cells lacking ppGpp displayed markedly elevated levels of free Esigma(70) compared with wild-type cells and that the repression of ribosomal RNA expression and reduced growth rate of mutants with constitutively elevated levels of ppGpp can be suppressed by overproducing Esigma(70). We conclude that ppGpp modulates the levels of free Esigma(70) and that this is an integral part of the alarmone's means of regulating a trade-off between growth and maintenance.

A Proximal Promoter Element Required for Positive Transcriptional Control by Guanosine Tetraphosphate and DksA Protein during the Stringent Response

“…This was indeed the case; a 2-fold overproduction of RNAP induced relative expression from the uspA-N dsc promoter in exponential growing cells, similar to PrrnB P1, although the PuspA-P dsc was repressed in relative terms as described previously (Fig. 5E) (22).…”

“…Specifically, elevated levels of free RNAP increase relative transcription from rrnB P1 while decreasing transcription from PuspA (22). Decreasing RNAP gave the exact opposite effect (28).…”

“…Positive Regulation by ppGpp and DksA-In previous studies (22,52), we have analyzed a uspA promoter spanning 227 bp upstream and 163 bp downstream from the transcriptional start site. Here, we constructed a uspA promoter harboring only the four core elements as follows: the Ϫ10 region, the Ϫ35 region, the spacer region, and the sequence immediately downstream from the Ϫ10 element (Fig.…”

“…Thus, upon growth arrest the rapid increase in ppGpp concentration results in a robust redirection of transcription from proliferation-related genes (e.g. those encoding rRNA, tRNA, and ribosomal proteins) to maintenance-related genes, such as the universal stress proteins, uspA and C-G genes (22)(23)(24), amino acid biosynthetic genes (6), and genes requiring alternative factors for their transcription (25)(26)(27). In fact, cells unable to make ppGpp almost completely fail to respond to starvation, as evi-denced by the proteome of starved ⌬relA ⌬spoT double mutants being almost identical to that of exponentially growing cells (28).…”

“…Whether RNAP concentrations actually increase during a stringent response and whether promoters positively regulated by ppGpp/DksA have, in general, a low affinity for RNAP is not known. Measurements have shown that the levels of free RNAP are elevated rather than reduced in cells lacking ppGpp (22), and calculations suggest that the free RNAP concentration rises with increasing growth rates, i.e. with decreasing levels of ppGpp (39).…”