Bacteriophage P22 Antitermination boxB Sequence Requirements Are Complex and Overlap with Those of l

• Published in: Journal of bacteriology 2008-06, Vol.190 (12), p.4263-4271
• Main Authors: Cocozaki, Alexis I, Ghattas, Ingrid R, Smith, Colin A
• Format: Article
• Language: English
• Subjects: Bacteria; Phage l
• ISSN: 0021-9193; 1098-5530

Transcription antitermination in phages l and P22 uses N proteins that bind to similar boxB RNA hairpins in regulated transcripts. In contrast to the l N-boxB interaction, the P22 N-boxB interaction has not been extensively studied. A nuclear magnetic resonance structure of the P22 N peptide boxB sub(left) 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 l N, indicating that the requirements imposed on boxB by P22 N overlap those imposed by l N. Point mutations can dramatically alter boxB specificity between P22 and l N. A boxB specific for P22 N can be mutated to l N specificity by a series of single mutations via a bifunctional intermediate, as predicted by neutral theories of evolution.