Identity of the 5'-terminal RNA nucleotide sequence of the satellite tobacco necrosis virus and its helper virus: possible role of the 5'-terminus in the recognition by virus-specific RNA replicase.

A pancreatic ribonuclease digest of (14)C-labeled tobacco necrosis virus RNA was fractionated according to charge by column chromatography. Individual fractions were dephosphorylated with alkaline phosphatase and rechromatographed. The fraction, originally containing oligonucleotides with seven negative charges, separated into two components corresponding to five (-5) and two negative charges (-2). The -5 fraction was derived from the internal oligonucleotides while the -2 fraction must have originated from a 5'-pyrophosphorylated terminal trinucleotide. The sequence of this terminal trinucleotide was determined by column chromatography on DEAE-cellulose in a triethyl ammonium carbonate gradient, using the appropriate markers. The radioactivity chromatographed with a (ApGp)U marker. The order of the Ap and Gp was determined after ribonuclease T(1) and alkaline phosphatase digestion. The radioactivity in the product chromatographed with an ApG marker. The 5'-terminus of tobacco necrosis virus RNA was therefore determined as ppApGpUp..., which is identical to the terminus of the RNA of its satellite virus as previously determined (J. Mol. Biol., 38, 59 (1968); Science, 160, 1452 (1968)). The 5' pyrophosphate in both viruses was probably formed by an in vivo enzymatic removal of a gamma-phosphate from a triphosphate, and its presence in both viruses suggested a common site of synthesis. The identity of the 5'-terminal sequences is considered not to be fortuitous and is discussed from the standpoint of their role as a recognition site for the virus-specific RNA replicase.