[No authors listed]
In bacteria, one primary and multiple alternative sigma (Ï) factors associate with the RNA polymerase core enzyme (E) to form holoenzymes (EÏ) with different promoter recognition specificities. The alternative Ï factor RpoS/ÏS is produced in stationary phase and under stress conditions and reprograms global gene expression to promote bacterial survival. To date, the three-dimensional structure of a full-length free Ï factor remains elusive. The current model suggests that extensive interdomain contacts in a free Ï factor result in a compact conformation that masks the DNA-binding determinants of Ï, explaining why a free Ï factor does not bind double-stranded promoter DNA efficiently. Here, we explored the solution conformation of ÏS using amide hydrogen/deuterium exchange coupled with mass spectrometry, NMR, analytical ultracentrifugation and molecular dynamics. Our data strongly argue against a compact conformation of free ÏS Instead, we show that ÏS adopts an open conformation in solution in which the folded Ï2 and Ï4 domains are interspersed by domains with a high degree of disorder. These findings suggest that E binding induces major changes in both the folding and domain arrangement of ÏS and provide insights into the possible mechanisms of regulation of ÏS activity by its chaperone Crl.
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