Direct proteolytic control of an extracytoplasmic function RNA polymerase sigma factor

The survival of any microbe relies upon its ability to respond to environmental change. Use of Extra Cytoplasmic Function (ECF) RNA polymerase sigma (σ) factors is a major strategy enabling such signal transduction. Streptomyces species harbour a large number of ECF σ factors; nearly all of which regulate genes required for morphological differentiation and/or response to environmental stress, except for σ AntA , which regulates starter-unit biosynthesis in the production of antimycin, an anticancer compound. Unlike a canonical ECF σ factor, whose activity is regulated by a cognate anti-σ factor, σ AntA is an orphan, raising intriguing questions about how its activity may be controlled. Here, we reconstitute in vitro ClpXP proteolysis of σ AntA , but not a variant lacking a C-terminal di-alanine motif. Furthermore, we show that the abundance of σ AntA in vivo is enhanced by removal of the ClpXP recognition sequence, and that levels of the protein rise when cellular ClpP-protease activity is abolished. These data establish direct proteolysis as an alternative and thus far unique control strategy for an ECF RNA polymerase σ factor and expands the paradigmatic understanding of microbial signal transduction regulation.