Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains.
RNA ligases participate in repair, splicing, and editing pathways that either reseal broken RNAs or alter their primary structure. Bacteriophage T4 RNA ligase (gp63) is the best-studied member of this class of enzymes, which includes yeast tRNA ligase and trypanosome RNA-editing ligases. Here, we identified another RNA ligase from the bacterial domain--a second RNA ligase (Rnl2) encoded by phage T4. Purified Rnl2 (gp24.1) catalyzes intramolecular and intermolecular RNA strand joining through ligase-adenylate and RNA-adenylate intermediates. Mutational analysis identifies amino acids required for the ligase-adenylation or phosphodiester synthesis steps of the ligation reaction. The catalytic residues of Rnl2 are located within nucleotidyl transferase motifs I, IV, and V that are conserved in DNA ligases and RNA capping enzymes. Rnl2 has scant amino acid similarity to T4 gp63. Rather, Rnl2 exemplifies a distinct ligase family, defined by variant motifs, that includes the trypanosome-editing ligases and a group of putative RNA ligases encoded by eukaryotic viruses (baculoviruses and an entomopoxvirus) and many species of archaea. These findings have implications for the evolution of covalent nucleotidyl transferases and virus-host dynamics based on RNA restriction and repair.
Ho
C Kiong
CK
Molecular Biology Program, The Sloan-Kettering Institute, New York, NY 10021, USA.
Shuman
Stewart
S
D000255:Adenosine Triphosphate / Q000378:metabolism; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D017122:Bacteriophage T4 / Q000201:enzymology*; D002384:Catalysis; D020134:Catalytic Domain; D004247:DNA / Q000378:metabolism; D004260:DNA Repair; D004305:Dose-Response Relationship, Drug; D006863:Hydrogen-Ion Concentration; D007093:Imidazoles / Q000494:pharmacology; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D011062:Polynucleotide Adenylyltransferase / Q000378:metabolism; D011118:Polynucleotide Ligases / Q000737:chemistry* / Q000502:physiology*; D017434:Protein Structure, Tertiary; D011130:RNA Ligase (ATP) / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D011994:Recombinant Proteins / Q000378:metabolism; D014764:Viral Proteins / Q000737:chemistry* / Q000502:physiology*
D007093:Imidazoles; D011994:Recombinant Proteins; D014764:Viral Proteins; C029899:imidazole; D000255:Adenosine Triphosphate; D004247:DNA; D011062:Polynucleotide Adenylyltransferase; D011118:Polynucleotide Ligases; D011130:RNA Ligase (ATP); C467724:bacteriophage T4 RNA ligase 2