Morphing molecular specificities between Arm-peptide and NUT-RNA in the antitermination complexes of bacteriophages λ and P22

Abstract

Bacteriophage λ's N-protein includes a 17-amino-acid segment, Arm, rich in arginine and having specific affinity for a 15-nucleotide RNA stem-loop called BOX-B. Parallel but different Arm/BOX-B sequences in λ's cousin, phage P22, account for some of the type specificity that distinguishes λ from P22: the N of each works only with its cognate BOX-B in vivo. We find that the specificity of Nλ can be shifted gradually to that of N22 by substituting sets of particular amino acids from Arm 22 into Arm of Nλ. The determinative amino acids are generally those shown by nuclear magnetic resonance to contact BOX-B RNA; gain or loss of these contact amino acids is reasonably expected to contribute to the affinity of each amino acid sequence. Intermediate sequences may show no function with either BOX-B, or weak function with both BOX-Bλ and BOX-B22, the latter suggesting possible evolutionary paths for specificity shifts.