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 wt Hfq. The native gel analysis of the kinetics of (i) ³²P-labeled MgrR annealing to eptB133 in the absence of Hfq (A) or the presence of Hfq (C), and (ii) ³²P-labeled eptB133 annealing to MgrR in the absence of Hfq (B) or the presence of wt Hfq (D). The data from A, B, C, and D were analyzed globally, and the lines in the plots are the results of global fitting. The schemes on the right of the plots in C and D describe kinetically preferred competing pathways (blue arrows) based on the data from Table 4. Unbound MgrR is marked as M, unbound eptB133 as E, MgrR-eptB133 complex as ME, MgrR-Hfq complex as MH, eptB133-Hfq complex as HE, and MgrR-eptB133-Hfq ternary complex as MEH. MEHE and MEHM denote quaternary complexes formed in excess of unlabeled eptB133 or MgrR, respectively. The asterisk indicates a slower migrating band, which is interpreted as the dimeric form of ³²P-eptB133.