ATP Binding to the σ54-Dependent Activator XylRTriggers a Protein Multimerization Cycle Catalyzed by UAS DNA

Finally, there are also cases Consejo Superior de Investigaciones Científicas in which the A domain plays only a small role in transcrip-28049 Madrid tional activity, either because its control depends on an Spain additional factor (such as the NifA protein, regulated by NifL) (Austin et al., 1990; Berger et al., 1994) or because the A domain does not exist as such (as is the case with Summary HrpS) (Xiao et al., 1994). The signal reception module A is typically connected to the central portion of these The events that take place at the prokaryotic enhancer proteins through a flexible hinge domain called Q linker of the Pu promoter of Pseudomonas putida prior to (Wooton and Drumond, 1989). The central domains of the engagement of the ␴ 54-RNA polymerase (␴ 54-all ␴ 54-dependent proteins are highly conserved, since RNAP) have been studied in vitro. ATP hydrolysis by they interact with the ␴ 54-RNAP holoenzyme (Berger et XylR, the cognate regulator of the system, is preceded and the oligomeriza-multimerization, ATP hydrolysis might be followed by tion determinants (Porter et al., 1993; Flashner et al., a return to the nonmultimerized state. This notion is 1995) that are required for transcription initiation. Next supported further by the properties of mutant proteins to the central modules, the C-terminal domains are con-that seem to be frozen, in either the nonmultimerized nected to the rest of the protein by a linker of variable or the multimerized state, respectively. These results length, and they include a helix-turn-helix motif respon-support a cyclic mechanism of ATP-dependent asso-sible for the binding to DNA (North et al., 1993). ciation/dissociation of XylR at the promoter UAS that In spite of responding to very different stimuli, the ␴ 54-precedes any involvement of the polymerase in tran-dependent activators seem to share a common mecha-scription initiation. nism of transcriptional activation (Kustu et al., 1991). This family of proteins typically binds to distant up-Introduction stream target DNA sites (Reitzer and Magasanik, 1986). These must loop out, sometimes with the assistance of auxiliary proteins such as integration host factor (IHF) Bacterial promoters dependent on the sigma factor ␴ tion that involves the binding of cognate regulatory pro-Pé rez-Martín et al., 1994) or HU (Pé rez-Martín and de teins to upstream activating sequence (UAS) located Lorenzo, 1995a) to contact the ␴ 54-RNAP already bound >100 bp from the binding site of the RNA polymerase to the promoter (Su et …