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The heat shock response of Escherichia coli is regulated by the cellular level and the activity of σ32, an alternative sigma factor for heat shock promoters. FtsH, a membrane-bound AAA-type metalloprotease, degrades σ32 and has a central role in the control of the σ32 level. The ftsH null mutant was isolated, and establishment of the ΔftsH mutant allowed us to investigate control mechanisms of the stability and the activity of σ32 separately in vivo. Loss of the FtsH function caused marked stabilization and consequent accumulation of σ32 (≈20-fold of the wild type), leading to the impaired downregulation of the level of σ32. Surprisingly, however, ΔftsH cells express heat shock proteins only two- to threefold higher than wild-type cells, and they also show almost normal heat shock response upon temperature upshift. These results indicate the presence of a control mechanism that downregulates the activity of σ32 when it is accumulated. Overproduction of DnaK/J reduces the activity of σ32 in ΔftsH cells without any detectable changes in the level of σ32, indicating that the DnaK chaperone system is responsible for the activity control of σ32in vivo. In addition, CbpA, an analogue of DnaJ, was demonstrated to have overlapping functions with DnaJ in both the activity and the stability control of σ32.