ABSTRACTThe CarD-CarG complex controls various cellular processes in the bacteriumMyxococcus xanthusincluding fruiting body development and light-induced carotenogenesis. The CarD N-terminal domain, which defines the large CarD_CdnL_TRCF protein family, binds to CarG, a zinc-associated protein that does not bind DNA. The CarD C-terminal domain resembles eukaryotic high-mobility-group A (HMGA) proteins, and its DNA binding AT hooks specifically recognize the minor groove of appropriately spaced AT-rich tracts. Here, we investigate the determinants of the only known CarD binding site, the one crucial in CarD-CarG regulation of the promoter of thecarQRSoperon (PQRS), a light-inducible promoter dependent on the extracytoplasmic function (ECF) σ factor CarQ.In vitro, mutating either of the 3-bp AT tracts of this CarD recognition site (TTTCCAGAGCTTT) impaired DNA binding, shifting the AT tracts relative to PQRShad no effect or marginally lowered DNA binding, and replacing the native site by the HMGA1a binding one at the human beta interferon promoter (with longer AT tracts) markedly enhanced DNA binding.In vivo, however, all of these changes deterred PQRSactivation in wild-typeM. xanthus, as well as in a strain with the CarD-CarG pair replaced by theAnaeromyxobacter dehalogenansCarD-CarG (CarDAd-CarGAd). CarDAd-CarGAdis functionally equivalent to CarD-CarG despite the lower DNA binding affinityin vitroof CarDAd, whose C-terminal domain resembles histone H1 rather than HMGA. We show that CarD physically associates with RNA polymerase (RNAP) specifically via interactions with the RNAP β subunit. Our findings suggest that CarD regulates a light-inducible, ECF σ-dependent promoter by coupling RNAP recruitment and binding to a specific DNA site optimized for affinity and position.