Schematic model of interaction between DsrA and Hfq. In our present model all three DsrA domains are located on one face of the hexameric complex. The A/U-rich single-stranded region between Domains I and II (red line) might wrap around the inner diameter of the torus by analogy to the interaction between Sm-proteins and short poly(U) substrates (Toro et al. 2001). If both Domains I and II lie on the same face of Hfq, only a portion of the central cavity can be used for interaction with the U-rich region to avoid a steric clash between the 5′- and 3′-extensions from this primary binding site. The additional structural requirements we observe for tight binding of larger RNAs probably result from the need of RNA secondary structure elements to lie down against the rest of the hexamer face of Hfq. Two highly conserved residues (R15 and F41, shown in blue) could assist in this process by providing ionic interactions with the RNA. In our model, the formation of a dodecamer might bring together two RNAs, one bound to either face of the torus, thereby increasing the chances of interactions between the RNAs. Tertiary structure showing the coaxial stacking of Domains II and III of DsrA is purely speculative at this point. The regions of increased RNase V1 nuclease sensitivity (blue lines) or decreased RNase I cleavage (green lines) in the presence of Hfq are indicated. Note that the cleavage of nucleotide A27 by RNase V1 could be interpreted as this region forming a single-stranded helix (Lowman and Draper 1986).
