MicroReview: Growth versus maintenance: a trade‐off dictated by RNA polymerase availability and sigma factor competition?

Abstract

SummaryThe regulatory design of higher organisms is proposed to comprise a trade-off between activities devoted to reproduction and those devoted to cellular maintenance and repair. Excessive reproduction will inevitably limit the organism's ability to resist stress whereas excessively devoted stress defence systems may increase lifespan but reduce Darwinian fitness. The trade-off is arguably a consequence of limited resources in any one organism but the nature and identity of such limiting resources are ambiguous. Analysis of global control of gene expression in Escherichia coli suggests that reproduction and maintenance activities are also at odds in bacteria and that this antagonism may be a consequence of a battle between transcription factors for limiting RNA polymerase. The outcome of this battle is regulated and depends on the nutritional status of the environment, the levels of the alarmone ppGpp, and RNA polymerase availability. This paper reviews how the concentration of RNA polymerase available for transcription initiation may vary upon shifts between growth and growth-arrest conditions and how this adjustment may differentially affect genes whose functions relate to reproduction and maintenance.

Elevated levels of σ S inhibit biofilm formation in Escherichia coli: a role for the Rcs phosphorelay

“…The vast majority of s S -controlled genes are positively regulated by the sigma factor and, therefore, the absence of known s Sregulated genes in our suppressor analysis would suggest that the biofilm phenotype is not the result of changes in the expression of a single gene or locus. On the other hand, a significant number of genes are negatively regulated by s S , primarily as the result of competition between sigma factors (in particular s S and s 70 , the housekeeping sigma factor) for the core RNA polymerase enzyme (Ferenci, 2005;Nystrom, 2004). Many of these s S -repressed genes are associated with motility, a trait with a key role in biofilm formation (Weber et al, 2005).…”

Transfer RNA instability as a stress response inEscherichia coli: Rapid dynamics of the tRNA pool as a function of demand

“…Nutrient limitation triggers alterations in the activity and promoter preferences of RNA polymerase, and major changes in the cell's gene expression program prime the cell for maintenance and survival rather than growth. 58 Several starvation-regulated factors can directly influence transcription by RNA polymerase, including the alarmone ppGpp (binding at the β′-ω and the β′-DksA interfaces of RNA polymerase), 59,60 the small RNA 6S (binding the σ 70 -RNA polymerase holoenzyme) 61,62 and a number of protein factors (DksA, 63 alternative sigma factors, 64 and anti-sigma factors 65 ) (reviewed in ref. 66).…”

“…The specific nature of the starvation (i.e., the type of nutrient that has become limiting for growth) and the time spent under nutrient limiting conditions affect the accumulation of these modulators of transcription, presumably allowing cells to target their stress response to best compensate for the shortage of particular metabolites. 58,67-70 Similarly, we reckon that tRNA degradation may only be beneficial during exposure to a subset of the possible stressors a bacterium may encounter. In our study 14 (as in most other studies on the stringent response, reviewed in refs.…”

FliA expression analysis and influence of the regulatory proteins RpoN, FleQ and FliA on virulence and in vivo fitness in Legionella pneumophila

“…Via deletion of the sigma factor (σ 28 ) FliA, other sigma factors like σ 70 have access to a higher amount of free core RNA polymerases (Nyström 2004). …”