A Comparative Kinetic and Thermodynamic Perspective of the σ-Competition Model in Escherichia coli

Abstract

Transcription is the most fundamental step in gene expression in any living organism. Various environmental cues help in the maturation of core RNA polymerase (RNAP; α(2)ββ'ω) with different σ-factors, leading to the directed recruitment of RNAP to different promoter DNA sequences. Thus it is essential to determine the σ-factors that affect the preferential partitioning of core RNAP among various σ-actors, and the role of σ-switching in transcriptional gene regulation. Further, the macromolecular assembly of holo RNAP takes place in an extremely crowded environment within a cell, and thus far the kinetics and thermodynamics of this molecular recognition process have not been well addressed. In this study we used a site-directed bioaffinity immobilization method to evaluate the relative binding affinities of three different Escherichia coli σ-factors to the same core RNAP with variations in temperature and ionic strength while emulating the crowded cellular milieu. Our data indicate that the interaction of core RNAP-σ is susceptible to changes in external stimuli such as osmolytic and thermal stress, and the degree of susceptibility varies among different σ-factors. This allows for a reversible σ-switching from housekeeping factors to alternate σ-factors when the organism senses a change in its physiological conditions.

Molecular Time Sharing through Dynamic Pulsing in Single Cells

“…All sigma factors were coupled to one another exclusively through competition for limiting amounts of shared core RNAP (STAR Methods). Such competition has been established in previous work ( Ganguly and Chatterji, 2012 ; Grigorova et al, 2006 ; Hicks and Grossman, 1996 ; Maeda et al, 2000 ), and is further supported by experiments in which ectopic expression of σ B repressed σ W and σ D activity under these conditions ( Figures S5A, S5B, and S5C ).…”

“…In bacteria, alternative sigma factors function as subunits of the RNAP holoenzyme, directing it to specific sets of target promoters ( Boylan et al, 1993 ; Helmann, 2002 , 2016 ; Paget, 2015 ; Price et al, 2001 ) ( Figure 1A ). In many contexts, alternative sigma factors actively compete for limiting amounts of RNAP ( Ganguly and Chatterji, 2012 ; Grigorova et al, 2006 ; Hicks and Grossman, 1996 ; Maeda et al, 2000 ). In addition to competition, alternative sigma factors are typically controlled through a multi-stage regulatory system with feedback.…”

Deciphering the essentiality and function of the anti‐σM factors in Bacillus subtilis

“…Sigma factors compete for a limited pool of RNAP core enzyme to transcribe their regulons (Maeda et al , ; Grigorova et al , ; Ganguly and Chatterji, ; Park et al , ). We reasoned that overexpression of SigA from an inducible promoter might compete with SigM and reduce its toxicity in the absence of its anti‐sigma factors.…”

Structured and Dynamic Disordered Domains Regulate the Activity of a Multifunctional Anti-σ Factor

“…3B ). We acknowledge that the difference in folded stability between these two σ/anti-σ complexes is relatively small; a more complete explanation of the inability of NepR SV to fully stabilize σ T in its closed, inactive form will likely require a better understanding of concentrations and affinities of competing σ factors and solvent conditions in the cell during stress ( 25 ).…”