The binding of Class II sRNA MgrR to two different sites on matchmaker protein Hfq enables efficient competition for Hfq and annealing to regulated mRNAs

Global modeling of MgrR annealing to eptB133 in the presence of Hfq variants with mutations in the distal, proximal, and rim RNA binding sites. The native gel analysis of the kinetics of (i) ³²P-labeled MgrR annealing to eptB133 in the presence of Hfq Y25D (A), Hfq K56A (C), or Hfq R16A (E), and (ii) ³²P-labeled eptB133 annealing to MgrR in the presence of Hfq Y25D (B), Hfq K56A (D), or Hfq R16A (F). The data for each of the Hfq mutants were analyzed globally with the data for the annealing in the absence of Hfq (Fig. 5A,B) (see Materials and Methods), and the lines in the plots are the results of global fitting. The schemes on the right of each plot describe kinetically preferred competing pathways (blue arrows) based on the data from Table 4. The RNAs and their complexes are marked in the same way as in Figure 5.