Altered 3'-terminal RNA structure in phage Q beta adapted to host factor-less Escherichia coli

The RNA phage Q beta requires for the replication of its genome an RNA binding protein called Q beta host factor or Hfq protein, Our previous results suggested that this protein mediates the access of replicase to the 3'-end of the Q beta plus strand RNA, Here we report the results of an evolutionary experiment in which phage Q beta was adapted to an Escherichia coli Q13 host strain with an inactivated host factor (hfq) gene. This strain initially produced phage at a titer approximate to 10,000-fold lower than the wild-type strain and with minute plaque morphology, but after 12 growth cycles, phage titer and plaque size had evolved to levels near those of the wild-type host. RNAs isolated from adapted Q beta mutants were efficient templates for replicase without host factor in vitro, Electron microscopy showed that mutant RNAs, in contrast to wild-type RNA, efficiently interacted with replicase at the 3'-end in the absence of host factor, The same set of four mutations in the 3'-terminal third of the genome was found in several independently evolved phage clones. One mutation disrupts the base pairing of the 3'-terminal CCCOH sequence, suggesting that the host factor stimulates activity of the wild-type RNA template by melting out its 3'-end.