Bacteriophage P22 Antitermination boxB Sequence Requirements Are Complex and Overlap with Those of [lamda]

Transcription antitermination in phages ... and P22 uses N proteins that bind to similar boxB RNA hairpins in regulated transcripts. In contrast to the ... N-boxB interaction, the P22 N-boxB interaction has not been extensively studied. A nuclear magnetic resonance structure of the P22 N peptide ... complex and limited mutagenesis have been reported but do not reveal a consensus sequence for boxB. We have used a plasmid-based antitermination system to screen boxBs with random loops and to test boxB mutants. We find that P22 N requires boxB to have a GNRA-like loop with no simple requirements on the remaining sequences in the loop or stem. U:A or A:U base pairs are strongly preferred adjacent to the loop and appear to modulate N binding in cooperation with the loop and distal stem. A few GNRA-like hexaloops have moderate activity. Some boxB mutants bind P22 and ... N, indicating that the requirements imposed on boxB by P22 N overlap those imposed by ... N. Point mutations can dramatically alter boxB specificity between P22 and ... N. A boxB specific for P22 N can be mutated to ... N specificity by a series of single mutations via a bifunctional intermediate, as predicted by neutral theories of evolution. (ProQuest: ... denotes formulae/symbols omitted.)