HK022 Nun Requires Arginine-Rich Motif Residues Distinct from λ N.
Bacteriophage λ N protein binds boxB RNA hairpins in the nut (N utilization) sites of immediate early λ transcripts and interacts with host factors to suppress transcriptional termination at downstream terminators. In opposition to λ N, the Nun protein of HK022 binds the boxBs of coinfecting λ transcripts, interacts with a similar or identical set of host factors, and terminates transcription to suppress λ replication. Comparison of N-boxB and Nun-boxB nuclear magnetic resonance (NMR) structural models suggests similar interactions, though limited mutagenesis of Nun is available. Here, libraries of Nun's arginine-rich motif (ARM) were screened for the ability to exclude λ coinfection, and mutants were assayed for Nun termination with a boxB plasmid reporter system. Several Nun ARM residues appear to be immutable: Asp26, Arg28, Arg29, Arg32, Trp33, and Arg36. Asp26 and Trp33 appear to be unable to contact boxB and are not found at equivalent positions in λ N ARM. To understand if the requirement of Asp26, Trp33, and Arg36 indicated differences between HK022 Nun termination and λ N antitermination complexes, the same Nun libraries were fused to the activation domain of λ N and screened for clones able to complement N-deficient λ. Mutants were assayed for N antitermination. Surprisingly, Asp26 and Trp33 were still essential when Nun ARM was fused to N. Docking suggests that Nun ARM contacts a hydrophobic surface of the NusG carboxy-terminal domain containing residues necessary for Nun function. These findings indicate that Nun ARM relies on distinct contacts in its ternary complex and illustrate how protein-RNA recognition can evolve new regulatory functions.


OBJECTIVE
λ N protein interacts with host factors to allow λ nut-containing transcripts to elongate past termination signals. A competing bacteriophage, HK022, expresses Nun protein, which causes termination of λ nut transcripts. λ N and HK022 Nun use similar arginine-rich motifs (ARMs) to bind the same boxB RNAs in nut transcripts. Screening libraries of Nun ARM mutants, both in HK022 Nun and in a λ N fusion, revealed amino acids essential to Nun that could bind one or more host factors. Docking suggests that NusG, which is present in both Nun termination and N antitermination, is a plausible partner. These findings could help understand how transcription elongation is regulated and illustrate how subtle differences allow ARMs to evolve new regulatory functions.
Department of Biology, American University of Beirut, Beirut, Lebanon.
Caroline S
CS
Tawk
Department of Biology, American University of Beirut, Beirut, Lebanon.
Ingrid R
IR
Ghattas
Department of Biology, American University of Beirut, Beirut, Lebanon colin.smith@aub.edu.lb.
Colin A
CA
Smith
D020816:Amino Acid Motifs / Q000502:physiology*; D000595:Amino Acid Sequence; D001120:Arginine / Q000737:chemistry*; D010582:Bacteriophage lambda / Q000378:metabolism*; D001483:Base Sequence; D015967:Gene Expression Regulation, Viral / Q000502:physiology*; D008958:Models, Molecular; D019151:Peptide Library; D011487:Protein Conformation; D014158:Transcription, Genetic; D054334:Viral Regulatory and Accessory Proteins / Q000378:metabolism*
C059417:N protein, Bacteriophage lambda; D019151:Peptide Library; D054334:Viral Regulatory and Accessory Proteins; D001120:Arginine