title: 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.
authors.affiliation: Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
authors.forename: Abantika
authors.initials: A
authors.lastname: Ganguly
authors.forename: Dipankar
authors.initials: D
authors.lastname: Chatterji
mesh_terms: D000388:Air; D001667:Binding, Competitive; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology / Q000378:metabolism* / Q000502:physiology; D029968:Escherichia coli Proteins / Q000378:metabolism*; D018869:Heat-Shock Response; D007700:Kinetics; D008954:Models, Biological; D009995:Osmosis; D012808:Sigma Factor / Q000378:metabolism*; D020349:Surface Plasmon Resonance; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D029968:Escherichia coli Proteins; D012808:Sigma Factor; D014867:Water; D012321:DNA-Directed RNA Polymerases